Useful bioinformatics software, tools, pipelines and workflows

Some of the million tools that are out there

Every now and then, I come across papers describing new tools and software (mainly) for some kind of metagenomics, amplicon (aka metabarcoding), genome related analysis and other things that interest me. Even though I might not need them at that particular moment, I make a note in case I would like to use them in a future project.

So, without further ado, here is what I have gathered so far. Of course, some of the tools may not be maintained anymore. And, it goes without saying, this is a non-exhaustive list of software; for sure there are twice as more out there that I have missed. Also, this list doesn’t include tools that I have been part of their development (one way or the other), such as PEMA, DARN and metaGOflow.

Software	Aim	Doi	Source code/Website
RiboViz	analyzing and visualizing ribosome profiling datasets	10.1186/s12859-017-1873-8	https://github.com/shahpr/RiboViz
GAIA 2.0	metagenomics analysis		https://www.gaia.sequentiabiotech.com/
BURRITO	interactive visualization of the links between taxonomic composition and function in microbiome datasets	10.3389/fmicb.2018.00365	https://github.com/borenstein-lab/burrito
paprica	metabolic inference from 16S rRNA gene sequence libraries / PAthway PRediction by phylogenetIC plAcement	10.1371/journal.pone.0135868	https://github.com/bowmanjeffs/paprica
LotuS	lightweight complete 16S pipeline	10.1186/2049-2618-2-30	http://psbweb05.psb.ugent.be/lotus/
BioSurfDB	biological compounds and mechanisms involved in biosurfactant production and/or biodegradation	10.1093/database/bav033	http://www.biosurfdb.org/
metabolic-hmms	HMM databases for microbial metabolic genes of environmental/biogeochemical importance		https://github.com/banfieldlab/metabolic-hmms
T-Coffee Server	collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures	10.1006/jmbi.2000.4042	http://www.tcoffee.org/
FWMFG (Freshwater microbial field guide)	freshwater 16S rRNA gene sequence database	10.1128/MMBR.00028-10	https://github.com/mcmahon-uw/FWMFG
TaxAss	Taxonomy Assignment workflow for 16S datasets	10.1101/214288	https://github.com/McMahonLab/TaxAss
Langille Lab PICRUSt Galaxy Instance (Correct for copy number variation)	Galaxy version Langille Lab		http://galaxy.morganlangille.com/
Hutlab	Galaxy version Huttenhower Lab		http://huttenhower.sph.harvard.edu/galaxy/root
microPITA (Picking Interesting Taxonomic Abundance)	computational tool enabling sample selection in two-stage (tiered) studies	10.1038/ismej.2013.139	http://huttenhower.sph.harvard.edu/micropita
CIPRES Science Gateway	inference of large phylogenetic trees		https://www.phylo.org/
robustness	microbial community taxa-function robustness estimation pipeline		https://github.com/borenstein-lab/robustness
Phinch	interactive, exploratory data visualization framework for –Omic datasets	10.1101/009944	http://phinch.org/index.html
ETE Toolkit	Phylogenetic tree (newick) viewer	10.1093/molbev/msw046	http://etetoolkit.org/treeview/
seqenv	Assign environment ontology (EnvO) terms to short DNA sequences	10.7717/peerj.2690	https://github.com/xapple/seqenv
SparCC	computing correlations in compositional data (16S, metagenomics, etc’).	10.1371/journal.pcbi.1002687	https://bitbucket.org/yonatanf/sparcc
micca	MICrobial Community Analysis	10.1038/srep09743	http://micca.org/
Perl-Bioinformatics-Scripts	Perl-Bioinformatics-Scripts		https://github.com/BryanChim/Perl-Bioinformatics-Scripts
Perl Scripts for bioinformatics	Perl Scripts for bioinformatics		http://bioinforma.weebly.com/perl-for-bioinformatics.html#/
FaBox	online fasta sequence toolbox		http://users-birc.au.dk/biopv/php/fabox/
16S rRNA Pyrosequencing Process Utilities	16S rRNA Pyrosequencing Process Utilities		http://alrlab.research.pdx.edu/aquificales/bioinformatics_scripts.html
microDB	database that aims to provide the most complete census to-date of the environmental distribution of prokaryotes	10.1111/j.1758-2229.2009.00030.x	http://botero.cnb.csic.es/envDB/
Volcano Plot	Volcano Plot		https://paolo.shinyapps.io/ShinyVolcanoPlot/
copynum_estimation	Software for copy number and organismal abundance estimation	10.1371/journal.pcbi.1002743	http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002743#s5
R script to determine the minimum number of sequences required for reliable microbial community analysis	A novel method to determine the minimum number of sequences	10.1016/j.mimet.2017.06.006	https://www.sciencedirect.com/science/article/pii/S0167701217301562
CopyRighter	improving the accuracy of microbial community profiles through lineage-specific gene copy number correction	10.1186/2049-2618-2-11	https://github.com/fangly/AmpliCopyrighter/
rrnDB	interpreting rRNA gene abundance in bacteria and archaea	10.1093/nar/gku1201	https://rrndb.umms.med.umich.edu/
mockrobiota	a public resource for sharing, validating, and documenting mock community data resources	10.1128/mSystems.00062-16	http://caporaso-lab.github.io/mockrobiota/
Metadex	The Metagenomic Data Explorer		https://search.proquest.com/openview/3e734d930740f85542e4bd14ee1ca762/1?pq-origsite=gscholar&cbl=18750&diss=y
TAXXI	Taxonomy cross-validation by identity	10.7717/peerj.4652	https://github.com/rcedgar/taxxi
NGLess	NGS Processing with Less Work	10.1186/s40168-019-0684-8	https://ngless.embl.de/
MASAME	MASAME	10.1111/1574-6941.12437	https://github.com/pbuttigieg/masame
MicrO	A Microbial Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions		https://github.com/pbuttigieg/MicrO
MicroPIE	Microbial Phenomics Information Extractor	10.1186/s12859-016-1396-8	https://github.com/biosemantics/micropie2
PrimerProspector	de novo design and taxonomic analysis of barcoded polymerase chain reaction primers	10.1093/bioinformatics/btr087	http://pprospector.sourceforge.net/
tax2tree	automatically decorating taxonomy onto a phylogenetic tree	10.1038/ismej.2011.139	http://tax2tree.sourceforge.net
SitePainter	interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context	10.1093/bioinformatics/btr685	http://biocore.github.io/SitePainter/
PATRIC	integrated data and analysis tools to support biomedical research on bacterial infectious diseases	10.1093/nar/gkw1017	https://www.patricbrc.org/
NINJA-OPS	Not Just Another - OTU Picking Solution	10.1371/journal.pcbi.1004658	https://github.com/GabeAl/NINJA-OPS
BugBase	measuring high-level phenotypes in your microbiome	10.1101/133462	https://bugbase.cs.umn.edu/index.html
DAS	Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy	10.1038/s41564-018-0171-1	https://github.com/cmks/DAS_Tool
WHAM! (Workflow Hub for Automated Metagenomic Exploration)	a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data	10.1186/s12864-018-4870-z	https://github.com/ruggleslab/jukebox/tree/master/wham_v1
SqueezeM	metagenomic analysis pipeline from reads tobins	10.1101/347559	https://github.com/jtamames/SqueezeM
SAMSA2	standalone metatranscriptome analysis pipeline	10.1186/s12859-018-2189-z	https://github.com/transcript/samsa2
BlastKOALA	Automatic annotation and KEGG mapping server suitable for functional characterization of complete genomes	10.1016/j.jmb.2015.11.006	https://www.kegg.jp/blastkoala/
GhostKOALA	Automatic annotation and KEGG mapping server suitable for functional characterization of metagenomes	10.1016/j.jmb.2015.11.006	https://www.kegg.jp/ghostkoala/
PAIPline	Pathogen identification in metagenomic and clinical next generation sequencing samples		https://gitlab.com/andreas.andrusch/paipline
Carnelian	Enhanced functional profiling of whole metagenome sequencing reads	10.1101/375121	http://cb.csail.mit.edu/cb/carnelian/
DAFGA	Diversity analysis of functional gene amplicons	10.1093/bioinformatics/btu394	https://github.com/outbig/DAFGA
COGNIZER	A Framework for Functional Annotation of Metagenomic Datasets	10.1371/journal.pone.0142102	http://metagenomics.atc.tcs.com/cognizer, https://metagenomics.atc.tcs.com/function/cognizer
WebMGA	a customizable web server for fast metagenomic sequence analysis	10.1186/1471-2164-12-444	http://weizhongli-lab.org/metagenomic-analysis
gcMeta	a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data	10.1093/nar/gky1008	https://gcmeta.wdcm.org/
CheckM	assessing the quality of genomes recovered from isolates, single cells, or metagenomes	10.1101/gr.186072.114	http://ecogenomics.github.io/CheckM/
dRep	Rapid and accurate comparison and de-replication of microbial genomes	10.1038/ismej.2017.126	https://github.com/MrOlm/drep
FLASH	Fast Length Adjustment of SHort reads	10.1093/bioinformatics/btr507	https://ccb.jhu.edu/software/FLASH/
Btrim	adapter and quality trimming	10.1016/j.ygeno.2011.05.009	http://graphics.med.yale.edu/trim/
SPIEC-EASI	Sparse and Compositionally Robust Inference of Microbial Ecological Networks	10.1371/journal.pcbi.1004226	https://github.com/zdk123/SpiecEasi
OTUX	V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes	10.1093/dnares/dsy045	https://web.rniapps.net/otux/
iVikodak	A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities	10.3389/fmicb.2018.03336	https://web.rniapps.net/iVikodak/
ranacapa	eDNA Data exploration		https://gauravsk.shinyapps.io/ranacapa/
ANCOM	Analysis of Composition of Microbiomes	10.3402/mehd.v26.27663	https://sites.google.com/site/siddharthamandal1985/research
MNEMONIC	MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations	10.1186/s12859-019-2623-x	https://gitlab.com/wrenlab/mnemonic
FENNEC	Functional Exploration of Natural Networks and Ecological Communities	10.1111/2041-210X.13060	https://fennec.molecular.eco/default_data/startpage
FunGuild	An open annotation tool for parsing fungal community datasets by ecological guild	10.1016/j.funeco.2015.06.006	https://github.com/UMNFuN/FUNGuild
FAPROTAX	Functional Annotation of Prokaryotic Taxa	10.1126/science.aaf4507	http://www.loucalab.com/archive/FAPROTAX/
Bcdatabaser	on-the-fly reference database creation for (meta-)barcoding	10.1093/bioinformatics/btz960	https://github.com/molbiodiv/bcdatabaser
SLIM	A web app for environmental DNA metabarcoding analysis	10.1186/s12859-019-2663-2	https://trtcrd.github.io/SLIM/
PIPITS	An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform	10.1111/2041-210X.12399	https://github.com/hsgweon/pipits
mOTUs2	profile a metagenomic or metatranscriptomic sample	10.1038/s41467-019-08844-4	https://motu-tool.org/
Cascabel	pipeline designed to run amplicon sequence analysis	10.1101/809384	https://github.com/AlejandroAb/CASCABEL
proGenomes3	improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes	10.1093/nar/gkz1002	http://progenomes.embl.de/
Kelpie	Generating full-length ‘amplicons’ from whole-metagenome datasets	10.7717/peerj.6174	https://github.com/PaulGreenfieldOz/WorkingDogs/tree/master/Kelpie
PhenDB	Prediction of bacterial phenotypes	10.1186/1471-2105-16-S14-S1	https://phendb.csb.univie.ac.at/
phyloFlash	Rapid SSU rRNA profiling and targeted assembly from metagenomes	10.1101/521922	https://github.com/HRGV/phyloFlash
Shade_CurrOpinMicro	Containing script for investigating core microbiota	10.1016/j.mib.2019.09.008	https://github.com/ShadeLab/PAPER_Shade_CurrOpinMicro
PMBD	a Comprehensive Plastics Microbial Biodegradation Database	10.1093/database/baz119	http://pmbd.genome-mining.cn/home/
MAR databases	a collection of richly annotated and manually curated contextual (metadata) and sequence databases	10.1093/nar/gkx1036	https://mmp.sfb.uit.no/databases/
iMicrobe	Tools and data-driven discovery platform for the microbiome sciences	10.1093/gigascience/giz083	https://www.imicrobe.us/
MelonnPan	Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences	10.1038/s41467-019-10927-1	http://huttenhower.sph.harvard.edu/melonnpan
Melon	metagenomic long-read-based taxonomic identification and quantification using marker genes	10.1186/s13059-024-03363-y	https://github.com/xinehc/melon
FeGenie	Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies	10.3389/fmicb.2020.00037	https://github.com/Arkadiy-Garber/FeGenie
NG-Tax	pipeline for 16S rRNA gene amplicon sequencing data	10.12688/f1000research.9227.2	https://github.com/JavierRamiroGarcia/NG-Tax
MetaShot	taxon classification of host-associated microbiome from shotgun metagenomic data	10.1093/bioinformatics/btx036	https://github.com/bfosso/MetaShot
LEMMI	A Live Evaluation of Computational Methods for Metagenome Investigation	10.1101/507731	https://lemmi.ezlab.org/
proGenomes2	annotated bacterial and archaeal genomes	10.1093/nar/gkz1002	http://progenomes.embl.de/
SOBA	sequence ontology bioinformatics analysis	10.1093/nar/gkq426	http://www.sequenceontology.org/cgi-bin/soba.cgi
CARD 2020	antibiotic resistance database	10.1093/nar/gkz935	https://card.mcmaster.ca
MEGARes	Antimicrobial Database for High-Throughput Sequencing	10.1093/nar/gkw1009	https://megares.meglab.org/
Metazen	metadata capture for metagenomes	10.1186/1944-3277-9-18	https://github.com/MG-RAST/metazen
Lathe	A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing	10.1038/s41587-020-0422-6	https://github.com/bhattlab/lathe
Metagenomics Workflows	Workflows for metagenomic sequence data processing and analysis	10.1038/s41587-020-0422-6	https://github.com/bhattlab/metagenomics_workflows
StrainSifter	bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s)		https://github.com/bhattlab/StrainSifter
MicrobiomeBestPracticeReview	Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing	10.1093/bib/bbz155	https://github.com/grimmlab/MicrobiomeBestPracticeReview
BacPipe	whole genome sequencing pipeline for clinical diagnostic bacteriology and outbreak detection	10.1016/j.isci.2019.100769	https://github.com/wholeGenomeSequencingAnalysisPipeline/BacPipe
Jovian	Metagenomics/viromics pipeline		https://github.com/DennisSchmitz/Jovian
Evergreen	Large scale automated phylogenomic analysis of bacterial whole-genome isolates	10.1101/540138	https://cge.cbs.dtu.dk/services/Evergreen
RIEMS	Reliable Information Extraction from Metagenomic Sequence datasets		https://github.com/EBI-COMMUNITY/fli-RIEMS
PIA (Phylogenetic Intersection Analysis)	Taxonomic Assignment of Metagenomic Data	10.3389/fevo.2020.00084	https://github.com/Allaby-lab/PIA
PhyloPhlAn	Precise phylogenetic analysis of microbial isolates and genomes from metagenomes		https://github.com/biobakery/phylophlan
Link-HD	an R package to integrate multiple heterogeneous datasets based on STATIS / a versatile framework to explore and integrate heterogeneous microbial communities	10.1093/bioinformatics/btz862	https://lauzingaretti.github.io/LinkHD-examples/
MicrobiomeAnalyst	comprehensive statistical, visual and meta-analysis of microbiome data	10.1093/nar/gkx295 ; 10.1038/s41596-019-0264-1	https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/home.xhtml
decontam	Identifying contaminants in marker-gene and metagenomics data	10.1186/s40168-018-0605-2	https://benjjneb.github.io/decontam/vignettes/decontam_intro.html
GMPR	Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data		https://github.com/jchen1981/GMPR
MetaLonDA	METAgenomic LONgitudinal Differential Abundance method	10.1186/s40168-018-0402-y	https://cran.r-project.org/web/packages/MetaLonDA/vignettes/MetaLonDA.html
MetaBAT 2	an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies	10.7717/peerj.7359	https://bitbucket.org/berkeleylab/metabat/src/master/
FunGeCo	web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information	10.1093/bioinformatics/btz957	https://web.rniapps.net/fungeco/
TAX CREdiT data	TAXonomic ClassifieR Evaluation Tool data repository	10.1186/s40168-018-0470-z	https://github.com/caporaso-lab/tax-credit-data
Metagenome-Assembled Genomes Orchestra (MAGO)	computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes	10.1093/molbev/msz237	http://mago.fe.uni-lj.si/
RFPlasmid	Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers		https://github.com/aldertzomer/RFPlasmid
Phage_tools			https://github.com/sxh1136/Phage_tools
GlobalFungi	Global database of fungal records from high-throughput-sequencing metabarcoding studies	10.1101/2020.04.24.060384	http://globalfungi.com/
CAMITAX	Taxon labels for microbial genomes	10.1093/gigascience/giz154	https://github.com/CAMI-challenge/CAMITAX
AutoTax	Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment provide species-level resolution	10.1101/672873	https://github.com/KasperSkytte/AutoTax
fSSU	Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias	10.1038/nbt.4045	https://github.com/MadsAlbertsen/fSSU
barrnap	BAsic Rapid Ribosomal RNA Predictor		https://github.com/tseemann/barrnap
MicrobiomeAnalyst	comprehensive statistical, functional, and meta-analysis of microbiome data	10.1038/s41596-019-0264-1	https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/
Ocean Gene Atlas	exploring the biogeography of plankton genes online	10.1093/nar/gky376	http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/
SHOGUN	modular, accurate, and scalable framework for microbiome quantification	10.1093/bioinformatics/btaa277	https://github.com/knights-lab/SHOGUN
MetaDEGalaxy	Galaxy workflow for differential abundance analysis of 16s metagenomic data	10.12688/f1000research.18866.2
MACADAM database	MetAboliC pAthways DAtabase for Microbial taxonomic groups	10.1093/database/baz049	https://github.com/maloleboulch/MACADAM-Database
CAMISIM	simulating metagenomes and microbial communities	10.1186/s40168-019-0633-6	https://github.com/CAMI-challenge/CAMISIM
PhyloPythiaS+	rapid reconstruction of low-ranking taxonomic bins from metagenomes	10.7717/peerj.1603	https://github.com/algbioi/ppsp/wiki
MBGD	Microbial Genome Database	10.1093/nar/gky1054	http://mbgd.genome.ad.jp/
FVE-novel	Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data	10.21203/rs.3.rs-17154/v1	https://github.com/saima-tithi/FVE-novel
VirFinder	identifying viral sequences from assembled metagenomic data	10.1186/s40168-017-0283-5	https://github.com/jessieren/VirFinder
Prokaryotic Virus Orthologous Groups (pVOGs)	a resource for comparative genomics and protein family annotation	10.1093/nar/gkw975	http://dmk-brain.ecn.uiowa.edu/pVOGs/
VirSorter	mining viral signal from microbial genomic data	10.7717/peerj.985	https://github.com/simroux/VirSorter
Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm)	prokaryotic gene recognition and translation initiation site identification	10.1186/1471-2105-11-119	http://compbio.ornl.gov/prodigal/
TaxonTableTools	graphical user interface software to explore and visualise DNA metabarcoding data	10.1101/2020.08.24.264317	https://github.com/TillMacher/TaxonTableTools
VirHostMatcher-Net	A network-based integrated framework for predicting virus–prokaryote interactions	10.1093/nargab/lqaa044	https://github.com/WeiliWw/VirHostMatcher-Net
FROGS	Find, Rapidly, OTUs with Galaxy Solution	10.1093/bioinformatics/btx791	https://github.com/geraldinepascal/FROGS.git
ShotMAP	Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes	10.1371/journal.pcbi.1004573	https://github.com/sharpton/shotmap
STRONG	STrain Resolution ON assembly Graph	10.1101/2020.09.06.284828	https://github.com/chrisquince/STRONG
Cviewer	A Java-based statistical framework for integration of shotgun metagenomics with other omics technologies	10.1186/s40168-024-01834-9	https://github.com/KociOrges/cviewer
CONCOCT	unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads	10.1038/nmeth.3103	https://github.com/BinPro/CONCOCT
Prokka	rapid prokaryotic genome annotation	10.1093/bioinformatics/btu153	https://github.com/tseemann/prokka
CALOUR	exploratory and interactive microbiome analysis based on heatmaps	10.1128/mSystems.00269-18	https://github.com/biocore/calour
CAMITAX	Taxon labels for microbial genomes	10.1093/gigascience/giz154	https://github.com/CAMI-challenge/CAMITAX
BIOCOM-PIPE	characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons	10.1186/s12859-020-03829-3	https://doi.org/10.5281/zenodo.3678129
PathoFact	prediction of virulence factors and antimicrobial resistance genes in metagenomic data	10.1101/2020.03.24.006148	https://git-r3lab.uni.lu/laura.denies/PathoFact
ideel	quick test for interrupted ORFs in bacterial/microbial genomes		https://github.com/mw55309/ideel
SCATA	Sequence Clustering and Analysis of Tagged Amplicons	10.1139/cjm-2017-0099	https://scata.mykopat.slu.se/
Ananke	Clustering marker gene data by time-series patterns	10.7717/peerj.3812	https://github.com/beiko-lab/ananke
phyloFlash	rapid small-subunit rRNA profiling and targeted assembly from metagenomes	10.1128/mSystems.00920-20	https://github.com/HRGV/phyloFlash
bioBakery 3	Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities	10.1101/2020.11.19.388223	https://github.com/biobakery/biobakery/wiki , http://segatalab.cibio.unitn.it/tools/biobakery/
Tax4Fun2	prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences	10.1186/s40793-020-00358-7	https://github.com/bwemheu/Tax4Fun2
Docker pipelines	a collection of nextflow workflows related to nanopore data, taxonomy and antibiotic resistance	10.5281/zenodo.4030719	https://github.com/replikation/docker_pipelines
What_the_Phage	A scalable workflow for the identification and analysis of phage sequences	10.1101/2020.07.24.219899	https://github.com/replikation/What_the_Phage
Cascabel	Scalable and Versatile Amplicon Sequence Data Analysis Pipeline	10.3389/fgene.2020.489357	https://github.com/AlejandroAb/CASCABEL
CoMA	an intuitive and user-friendly pipeline for amplicon-sequencing data analysis	10.1371/journal.pone.0243241	https://www.uibk.ac.at/microbiology/services/coma.html
MARES	a replicable pipeline and curated reference database for marine eukaryote metabarcoding	10.1038/s41597-020-0549-9	https://github.com/wpearman1996/MARES_database_pipeline
LULU	A r-package for distribution based post clustering curation of amplicon data	10.1038/s41467-017-01312-x	https://github.com/tobiasgf/lulu
fusionDB	assessing microbial diversity and environmental preferences via functional similarity networks	10.1093/nar/gkx1060	https://services.bromberglab.org/fusiondb/
Vamb	Improved metagenome binning and assembly using deep variational autoencoders	10.1038/s41587-020-00777-4	https://github.com/RasmussenLab/vamb
eukaryotesV4 database	curated database of V4 region of 18S rDNA. It was built to extract and taxonomically classify short metagenomic reads (mTags)	10.1111/1755-0998.13147	https://github.com/aleixop/eukaryotesV4
EcolUtils	Utilities for community ecology analysis		https://github.com/GuillemSalazar/EcolUtils
Recurrence-Index	the R code for calculating the index		https://github.com/CaterinaRG/Recurrence-Index
DEMENTpy	A trait and individual based spatially explicit soil microbial systems modelling framework	10.1111/j.1461-0248.2012.01807.x	https://github.com/bioatmosphere/DEMENTpy
iDynoMiCS	Individual-based Dynamics of Microbial Communities Simuator	10.1111/j.1462-2920.2011.02414.x	https://www.birmingham.ac.uk/generic/idynomics/index.aspx
NUFEB	modelling and simulating microbial communities		https://github.com/nufeb/NUFEB
MicroMap	web application that can be used to map global microbial abundance		https://micromap.icm.csic.es/
scrapp	A tool to assess the diversity of microbial samples from phylogenetic placements	10.1111/1755-0998.13255	https://github.com/pbdas/scrapp
mgPipe	pipeline to integrate microbial abundances (coming from metagenomic data) with constraint-based modeling, creating individuals’ personalized models		https://github.com/opencobra/cobratoolbox/tree/master/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe
MIGA	Microbial Genomes Atlas Online	10.1093/nar/gky467	http://microbial-genomes.org/
enveomics collection	a toolbox for specialized analyses of microbial genomes and metagenomes	10.7287/peerj.preprints.1900v1	http://enve-omics.ce.gatech.edu/
PATO	Pangenome Analysis Toolkit	10.1101/2021.01.30.428878	https://github.com/irycisBioinfo/PATO
Protologger	all-in-one genome description tool, aimed at simplifying the process of gathering the data required for writing protologues		http://protologger.de/
MetaStorm	metagenomic analysis server	10.1371/journal.pone.0162442	http://bench.cs.vt.edu/MetaStorm/
NanoARG	Antimicrobial Resistance analysis for nanopore reads	10.1101/483248	http://bench.cs.vt.edu/nanoARG
ARGminer	Antibiotic Resistance Gene miner databasε		https://bench.cs.vt.edu/argminer
DeepARG	a deep learning approach for predicting antibiotic resistance genes from metagenomic data	10.1186/s40168-018-0401-z	https://bench.cs.vt.edu/deeparg_analyze/
eDNAFlow	automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity	10.1111/1755-0998.13356	https://github.com/mahsa-mousavi/eDNAFlow
refdb	A reference database manager for R		https://github.com/fkeck/refdb
bioseq	A Toolbox for Manipulating Biological Sequences in R	10.1111/2041-210X.13490	https://github.com/fkeck/bioseq
GAPeDNA	Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding	10.1111/ddi.13142	https://shiny.cefe.cnrs.fr/GAPeDNA/
AutoTax	automatically generates de novo taxonomy from full length 16S rRNA amplicon sequence variants (FL-ASVs)	10.1128/mBio.01557-20	https://github.com/KasperSkytte/AutoTax
Decona	From demultiplexing to consensus for Nanopore amplicon data		https://github.com/Saskia-Oosterbroek/decona
TaxonTableTools	analyse and visualize their metabarcoding data quickly and reproducible via a graphical user interface	10.1186/1471-2105-12-385	https://pypi.org/project/taxontabletools/
EasyMAP	user-friendly online platform for analyzing 16S ribosomal DNA sequencing data	10.1016/j.nbt.2021.03.001	http://easymap.cgm.ntu.edu.tw/
Natrix	open-source bioinformatics pipeline for the preprocessing of raw sequencing data	10.1186/s12859-020-03852-4	https://github.com/MW55/Natrix
LinDA	Linear Models for Differential Abundance Analysis of Microbiome Compositional Data	arXiv:2104.00242	https://github.com/zhouhj1994/LinDA
Natrix-Pipeline	preprocessing of raw sequencing data	10.1186/s12859-020-03852-4	https://github.com/zelezniak-lab/Natrix
KAIJU	Fast and sensitive taxonomic classification for metagenomics	10.1038/ncomms11257	http://kaiju.binf.ku.dk/server
DAnIEL	web server to analyze ITS amplicon sequencing data	10.1101/2021.04.12.437814	https://sbi.hki-jena.de/daniel/latest/
MiDAS Field Guide	An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters	10.1016/j.watres.2020.115955	https://www.midasfieldguide.org/guide/search
Calour	Interactive, Microbe-Centric Analysis Tool	10.1128/mSystems.00269-18	https://github.com/biocore/calour
microDecon	read‐subtraction tool for the post‐sequencing removal of contamination in metabarcoding studies	10.1002/edn3.11	https://github.com/donaldtmcknight/microDecon
JAMP	Just Another Metabarcoding Pipeline		https://github.com/VascoElbrecht/JAMP
chkMocks	Is the composition in experimental mock standards similar to theoretical expected composition		https://microsud.github.io/chkMocks/articles/aIntroduction.html
HCK and ABAA	Pipeline to Improve Fungi Metabarcoding Analysis	10.3389/fmicb.2021.640693	https://bitbucket.org/GottySG36/hck/src/master/
SHOGUN	profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data	10.1093/bioinformatics/btaa277	https://github.com/knights-lab/SHOGUN
MARES	pipeline and curated reference database for marine eukaryote metabarcoding	10.1038/s41597-020-0549-9	https://github.com/wpearman1996/MARES_database_pipeline
mTAGs	taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes	10.1093/bioinformatics/btab465	https://github.com/SushiLab/mTAGs
MiCoNE	Microbial Co-occurrence Network Explorer	10.1128/msystems.00961-22	https://github.com/segrelab/MiCoNE
Metage2Metabo	microbiota-scale metabolic complementarity for the identification of key species	10.7554/eLife.61968	https://github.com/AuReMe/metage2metabo , https://pypi.org/project/Metage2Metabo/
MetaWRAP	a flexible pipeline for genome-resolved metagenomic data analysis	10.1186/s40168-018-0541-1	https://github.com/bxlab/metaWRAP
metaMATE	metabarcoding Multiple Abundance Threshold Evaluator	10.1111/1755-0998.13337	https://github.com/tjcreedy/metamate
Meta-SourceTracker	application of Bayesian source tracking to shotgun metagenomics	10.7717/peerj.8783	https://github.com/residentjordan/SourceTracker2-diagnostics
AlienTrimmer	quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads	10.1016/j.ygeno.2013.07.011	ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
Blobology	exploring raw genome data for contaminants, symbionts, and parasites using taxon-annotated GC-coverage plots	10.3389/fgene.2013.00237	https://github.com/blaxterlab/blobology
Blobsplorer	aids exploration and selection of subsets from TAGC-annotated data	10.3389/fgene.2013.00237	https://github.com/mojones/Blobsplorer
SourceTracker	Bayesian community-wide culture-independent microbial source tracking	10.1038/nmeth.1650	https://sourceforge.net/projects/sourcetracker/
MetagenoNets	inference as well as visualization of categorical, integrated (inter-omic) and bi-partite networks	10.1093/nar/gkaa254	https://web.rniapps.net/metagenonets
DnoisE	distance denoising by entropy	10.7717/peerj.12758	https://github.com/adriantich/DnoisE
Multiqc	A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.	10.1093/bioinformatics/btw354	https://multiqc.info/
CONTIGuator	contigs mapping over a reference genome	10.1186/1751-0473-6-11	http://contiguator.sourceforge.net
GapFiller	close gaps within scaffolds using paired reads	10.1186/gb-2012-13-6-r56	https://sourceforge.net/projects/gapfiller/
Sealer	scalable gap-closing application for finishing draft genomes	10.1186/s12859-015-0663-4	https://github.com/bcgsc/abyss/tree/sealer-release
FGAP	automated gap closing tool	10.1186/1756-0500-7-371	https://github.com/pirovc/fgap
GAPPadder	closing gaps on draft genomes with short sequence reads	10.1186/s12864-019-5703-4	https://github.com/simoncchu/GAPPadder
PAGIT	post-assembly genome-improvement toolkit to obtain annotated genomes from contigs	10.1038/nprot.2012.068	https://www.sanger.ac.uk/tool/pagit/
CloG	a pipeline for closing gaps in a draft assembly using short reads	10.1109/ICCABS.2011.5729881
GapBlaster	Graphical Gap Filler for Prokaryote Genomes	10.1371/journal.pone.0155327	https://sourceforge.net/projects/gapblaster2015/
PGcloser	Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes	10.1177/1176934320913859
DENTIST	using long reads for closing assembly gaps at high accuracy	10.1093/gigascience/giab100	https://github.com/a-ludi/dentist
TGS-GapCloser	fast and accurate gap closer for large genomes	10.1093/gigascience/giaa094	https://github.com/BGI-Qingdao/TGS-GapCloser
MetaPlatanus	metagenome assembler that combines long-range sequence links and species-specific features	10.1093/nar/gkab831	https://github.com/rkajitani/MetaPlatanus
METAnnotatorX2	Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses	10.1128/mSystems.00583-21	http://probiogenomics.unipr.it/cmu/
nf-core/mag	best-practice pipeline for metagenome hybrid assembly and binning	10.1093/nargab/lqac007	https://github.com/nf-core/mag
MUFFIN	Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis	10.1371/journal.pcbi.1008716	https://github.com/RVanDamme/MUFFIN
Lathe	A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing	10.1038/s41596-020-00424-x	https://github.com/bhattlab/lathe
BusyBee	metagenomic data analysis by bootstrapped supervised binning and annotation	10.1093/nar/gkx348	https://ccb-microbe.cs.uni-saarland.de/busybee
MaSuRCA	genome assembler	10.1093/bioinformatics/btt476	https://github.com/alekseyzimin/masurca
MetaErg	An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs	10.3389/fgene.2019.00999	https://github.com/xiaoli-dong/metaerg
MAGpy	downstream analysis of metagenome-assembled genomes (MAGs)	10.1093/bioinformatics/bty905	https://github.com/WatsonLab/MAGpy
tidyMicro	a pipeline for microbiome data analysis and visualization using the tidyverse in R	10.1186/s12859-021-03967-2	https://github.com/CharlieCarpenter/tidyMicro
novelfams	Novel Microbial Gene Families	10.1101/2022.01.26.477801	https://novelfams.cgmlab.org/
AGNOSTOS-DB	a resource to unlock the uncharted regions of the coding sequence space	10.1101/2021.06.07.447314	https://github.com/functional-dark-side/agnostos-wf
MATAM	Reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes	10.1093/bioinformatics/btx644	https://github.com/bonsai-team/matam
marky-coco	pipeline based on de novo single-metagenome assembly for characterization of hgc genes	10.1101/2022.03.14.484253	https://github.com/ericcapo/marky-coco
KEGGDecoder-binder	To calculate metabolic pathway completeness and build heatmaps from GhostKOALA output via KEGGDecoder		https://github.com/rotheconrad/KEGGDecoder-binder
KEGGDecoder	parse through KEGG-Koala outputs (blastKOALA, ghostKOALA, KOFAMSCAN) to determine completeness of metabolic pathways	10.1038/s41396-018-0091-3	https://github.com/bjtully/BioData/tree/master/KEGGDecoder
MicrobeAnnotator	Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes.	10.1186/s12859-020-03940-5	https://github.com/cruizperez/MicrobeAnnotator
Functional Annotation			https://github.com/biovcnet/biovcnet.github.io/wiki/TOPIC:-Functional-Annotation
FastANI calculator			https://gtdb.ecogenomic.org/tools/fastani
MAG scripts	scripts used for MAGs for the Brazelton et al. manuscript on Lost City fluids MAGs		https://github.com/Brazelton-Lab/Brazelton-2022-Lost-City-fluids-MAGs/tree/main/scripts
IMP	Integrative Multi-species Prediction	10.1093/nar/gkv486	http://imp.princeton.edu/
GraPhlAn	Compact graphical representation of phylogenetic data and metadata	10.7717/peerj.1029	http://segatalab.cibio.unitn.it/tools/graphlan/
PropagAtE	Prophage Activity Estimator: estimating if a prophage is in the lytic or lysogenic stage of infection	10.1128/msystems.00084-22	https://github.com/AnantharamanLab/PropagAtE
M2M - metage2metabo	microbiota-scale metabolic complementarity for the identification of key species	10.7554/eLife.61968	https://github.com/AuReMe/metage2metabo
eQuilibrator	a database solution for thermodynamic constant estimation	10.1093/nar/gkab1106	https://equilibrator.weizmann.ac.il/
MicrobeAnnotator	Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes	10.1186/s12859-020-03940-5	https://github.com/cruizperez/MicrobeAnnotator
PhenDB	Prediction of microbial phenotypes based on comparative genomics	10.1186/1471-2105-16-S14-S1	https://phendb.org/
microeco	An R package for data mining in microbial community ecology	10.1093/femsec/fiaa255	https://github.com/ChiLiubio/microeco
Genomics Tutorial	Genomics Tutorial		https://genomics.sschmeier.com/introduction.html
RefSoil	A Reference Database for Genes and Traits of Soil Plasmids	10.1128/mSystems.00349-18	https://github.com/ShadeLab/RefSoil_plasmids
OGT_prediction	Predicting the optimal growth temperatures of prokaryotes using only genome derived features	10.1093/bioinformatics/btz059	https://github.com/DavidBSauer/OGT_prediction
Trait synthesis	A synthesis of bacterial and archaeal phenotypic trait data	10.1038/s41597-020-0497-4	https://github.com/bacteria-archaea-traits/bacteria-archaea-traits , https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/releases/tag/v1.0.0
Major dimensions	Cell size, genome size and maximum growth rate	10.1002/ece3.7290	https://github.com/bacteria-archaea-traits/major-dimensions , https://github.com/bacteria-archaea-traits/major-dimensions/releases/tag/v1.0.0
TEMPURA	Database of Growth TEMPeratures of Usual and Rare Prokaryotes	10.1264/jsme2.ME20074	http://togodb.org/db/tempura
tRNA thermometer	using tRNA sequence to predict OGT	10.1093/nar/gkaa1030	https://bitbucket.org/bucklerlab/cnn_trna_ogt/ , https://doi.org/10.25739/a0g2-wb14
KEMET	KEGG Module evaluation and microbial genome annotation expansion	10.1016/j.csbj.2022.03.015	https://github.com/Matteopaluh/KEMET
EukCC	estimation of eukaryotic genome quality in terms of completion and contamination, for the assessment of eukaryotic MAGs	10.1186/s13059-020-02155-4	https://github.com/Finn-Lab/EukCC
OrthoDB	hierarchical catalog of eukaryotic orthologs	10.1093/nar/gkm845	http://cegg.unige.ch/orthodb
PARSEC	localization and characterization of genomic sites in complete eukaryotic genomes
CulebrONT	long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes	10.1101/2021.07.19.452922	https://pypi.org/project/culebrONT/
Exogean	annotating protein-coding genes in eukaryotic genomic DNA	10.1186/gb-2006-7-s1-s7
QUAST-LG	genome assembly evaluation	10.1093/bioinformatics/bty266	http://cab.spbu.ru/software/quast-lg
Helixer	cross-species gene annotation of large eukaryotic genomes using deep learning	10.1093/bioinformatics/btaa1044	https://github.com/weberlab-hhu/Helixer
EukMetaSanity	prediction of eukaryote genomes	10.12688/f1000research.129161.1	https://github.com/cjneely10/EukMetaSanity
AMAW	automated gene annotation for nonmodel eukaryotic genomes	10.1101/2021.12.07.471566	https://bitbucket.org/phylogeno/amaw/
BiSCoT	improving large eukaryotic genome assemblies with optical maps	10.7717/peerj.10150	http://www.genoscope.cns.fr/biscot
diArk	a resource for eukaryotic genome research	10.1186/1471-2164-8-103	http://www.diark.org/
Tapestry	validate and edit small eukaryotic genome assemblies with long reads	10.1101/2020.04.24.059402	https://github.com/johnomics/tapestry
OPERA-LG	efficient and exact scaffolding of large, repeat-rich eukaryotic genomes	10.1186/s13059-016-0951-y	http://sourceforge.net/projects/operasf/
OrthoFiller	utilising data from multiple species to improve the completeness of genome annotations	10.1186/s12864-017-3771-x	https://github.com/mpdunne/orthofiller
Fluxer	web application for the computation and interactive visualization of flux graphs from genome-scale metabolic models		https://fluxer.umbc.edu/
ARGs-OAP	analysis pipeline for antibiotic resistance genes detection from metagenomic data	10.1093/bioinformatics/btw136	https://smile.hku.hk/SARGs
arg_ranker	detecting ARGs and assessing the ARG risks in metagenomes and genomes	10.1038/s41467-021-25096-3	https://github.com/caozhichongchong/arg_ranker
MICOM	metabolic modeling of microbial communities	10.1128/mSystems.00606-19	https://micom-dev.github.io/micom/
COMETS	computer simulations of metabolism in spatially structured microbial communities	10.1038/s41596-021-00593-3	https://www.runcomets.org/about
Xander	employing a novel method for efficient gene-targeted metagenomic assembly	10.1186/s40168-015-0093-6	https://github.com/rdpstaff/Xander_assembler
MiDAS 4	catalogue of full-length 16S rRNA gene sequences in wastewater treatment plants	10.1038/s41467-022-29438-7	https://www.midasfieldguide.org/guide
NMDC EDGE	metagenomic workflows		https://nmdc-edge.org/home
RecruitPlotEasy	Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population	10.3389/fbinf.2021.826701	https://github.com/KGerhardt/RecruitPlotEasy
antiSMASH 5.0	secondary metabolite genome mining pipeline	10.1093/nar/gkz310	https://antismash.secondarymetabolites.org/#!/start
GapMind	Automated annotation of Amino acid biosynthesis	10.1128/mSystems.00291-20	https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi
GapMind	Automated annotation of catabolism of small carbon sources	10.1101/2021.11.02.466981	https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi?set=carbon
Microbiome Maps	Hilbert Curve Visualizations of Metagenomic Profiles	10.1101/2021.03.22.436520	https://www.microbiomemaps.org/
Bactopia	complete analysis of bacterial genomes	10.1128/mSystems.00190-20	https://bactopia.github.io/v2.2.0/ ; https://bactopia.github.io/latest/
VirSorter2	customizable pipeline to identify viral sequences from (meta)genomic data		https://bitbucket.org/MAVERICLab/virsorter2/src/master/
namingGTDB		10.20944/preprints202111.0557.v1	https://github.com/quadram-institute-bioscience/namingGTDB
CoreGenomePrimers	Pangenome-guided primer design for clade-specific primer generation		https://github.com/leylabmpi/CoreGenomePrimers
MicRhoDE	a curated database for the analysis of microbial rhodopsin diversity and evolution	10.1093/database/bav080	http://application.sb-roscoff.fr/micrhode/
BacARscan	an in-silico resource to discern diversity in antibiotic resistance genes		https://github.com/University-of-Delhi-south-campus/BacARscan
MAGNETO	An Automated Workflow for Genome-Resolved Metagenomics	10.1128/msystems.00432-22	https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto
Tripal MapViewer	A tool for interactive visualization and comparison of genetic maps	10.1093/database/baz100	https://gitlab.com/mainlabwsu/tripal_map
BAC-BROWSER	Visualization and Analysis of Prokaryotic Genomes	10.3389/fmicb.2018.02827	http://smdb.rcpcm.org/tools/index.html
FLIM-MAP	Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways	10.3389/fmicb.2018.02183	https://web.rniapps.net/FlimMap/
AnnoTree	visualization and exploration of a functionally annotated microbial tree of life	10.1093/nar/gkz246	http://annotree.uwaterloo.ca/
SLING	a tool to search for linked genes in bacterial datasets	10.1093/nar/gky738	https://github.com/ghoresh11/sling/wiki
Balrog	A universal protein model for prokaryotic gene prediction	10.1371/journal.pcbi.1008727	https://github.com/salzberg-lab/Balrog
PATRIC	Pathosystems Resource Integration Center	10.1093/nar/gkz943	https://patricbrc.org/
coda4microbiome	Compositional Data Analysis for Microbiome Studies	10.1101/2022.06.09.495511v1	https://malucalle.github.io/coda4microbiome/
SAMBA	Standardized and Automated MetaBarcoding Analyses workflow		https://github.com/ifremer-bioinformatics/samba
SHOOT	phylogenetic gene search and ortholog inference	10.1186/s13059-022-02652-8	https://shoot.bio/
MarkerMAG	linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads	10.1093/bioinformatics/btac398	https://github.com/songweizhi/MarkerMAG
StrainXpress	strain aware metagenome assembly from short reads	10.1093/nar/gkac543	https://github.com/HaploKit/StrainXpress
Pseudofinder	detection of pseudogenes in prokaryotic genomes	10.1093/molbev/msac153	https://github.com/filip-husnik/pseudofinder
getSequenceInfo	a suite of tools allowing to get genome sequence information from public repositories	10.1186/s12859-022-04809-5	https://github.com/karubiotools/getSequenceInfo
Simka	de novo comparative metagenomics tool	10.7717/peerj-cs.94	https://github.com/GATB/simka
SqueezeMeta	a fully automated metagenomics pipeline, from reads to bins	10.3389/fmicb.2018.03349	https://github.com/jtamames/SqueezeMeta
metaGT	improving and quantification metatranscriptome assembly using metagenome data		https://github.com/ablab/metaGT
METABOLIC	METabolic And BiogeOchemistry anaLyses In miCrobes	10.1186/s40168-021-01213-8	https://github.com/AnantharamanLab/METABOLIC
MetaPop	a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations	10.1186/s40168-022-01231-0	https://github.com/metaGmetapop/metapop
Searching SRA	Similarity Searching the SRA		https://edwards.flinders.edu.au/similarity-searching-the-sra/
SituSeq	remote and offline analysis of Nanopore-generated 16S rRNA amplicon data	10.1038/s43705-023-00239-3	https://github.com/jkzorz/SituSeq
PhiSpy	identifies prophages in Bacterial (and probably Archaeal) genomes	10.1101/2023.04.20.537752	https://github.com/linsalrob/PhiSpy
PHANOTATE	annotate phage genomes		https://github.com/linsalrob/PHANOTATE
FOCUS	An Agile Profiler for Metagenomic Data	10.7717/peerj.425	https://github.com/linsalrob/FOCUS
mapDamage2.0	fast approximate Bayesian estimates of ancient DNA damage parameters	10.1093/bioinformatics/btt193	https://github.com/ginolhac/mapDamage
PyDamage	automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly	10.7717/peerj.11845	https://github.com/maxibor/pydamage
Fitness Browser	Browse thousands of genome-wide fitness experiments for diverse bacteria		https://fit.genomics.lbl.gov/
differential-abundance analysis	taxonomic bias and differential-abundance analysis	10.1101/2022.08.19.504330	https://github.com/mikemc/differential-abundance-theory
taxumap	Visualize structure in large microbiome datasets		https://github.com/jsevo/taxumap
GOOS BioEco Portal	information on ocean biological and ecosystem observations		https://bioeco.goosocean.org/
binny	an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets	10.1101/2021.12.22.473795	https://github.com/a-h-b/binny
medna-metadata	open-source data management system for tracking environmental DNA samples and metadata	10.1093/bioinformatics/btac556	https://github.com/Maine-eDNA/medna-metadata
phyloMDA	phylogeny-aware microbiome data analysis	10.1186/s12859-022-04744-5	https://github.com/liudoubletian/phyloMDA
POST	phylogeny-guided microbiome OTU-specific association test	10.1186/s40168-022-01266-3	https://cran.r-project.org/web/packages/POSTm/index.html
PMG = Principal Microbial Groups	a novel approach that groups OTUs based only on relative abundances as an alternative to taxon grouping	10.1093/bib/bbac328	https://github.com/asliboyraz/PMGs
DeepToA	An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome	10.1093/bioinformatics/btac584	https://plabase.informatik.uni-tuebingen.de/deeptoa/
mOTUlizer	a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation	10.1093/nargab/lqac060	https://github.com/moritzbuck/mOTUlizer
SECOM	Sparse Estimation of Correlations among Microbiomes for correlation analysis	10.1038/s41467-022-32243-x	https://www.bioconductor.org/packages/release/bioc/html/ANCOMBC.html
APSCALE	advanced pipeline for simple yet comprehensive analyses of DNA Meta-barcoding data	10.1093/bioinformatics/btac588	https://github.com/DominikBuchner/apscale
MetaMeta	integrating metagenome analysis tools to improve taxonomic profiling	10.1186/s40168-017-0318-y	https://github.com/pirovc/metameta/
PAIPline	Pipeline for the Automatic Identification of Pathogens		https://gitlab.com/andreas.andrusch/paipline
DaisySuite	pipeline for horizontal gene transfer (HGT) detection using sequencing data		https://gitlab.com/rki_bioinformatics/DaisySuite
gNOMO	a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms		https://gitlab.com/rki_bioinformatics/gnomo
phytools	Phylogenetic Tools for Comparative Biology (and Other Things)		https://CRAN.R-project.org/package=phytools
phytools 2.0	an updated R ecosystem for phylogenetic comparative methods	10.7717/peerj.16505	https://github.com/liamrevell/Revell.phytools-v2/
mixOmics	multivariate methods for the exploration and integration of biological datasets	10.1371/journal.pcbi.1005752	http://mixomics.org/
MixMC	Multivariate Statistical Framework to Gain Insight into Microbial Communities	10.1371/journal.pone.0160169	http://mixomics.org/mixMC/
magi	Metabolites and Genes Integrated		https://github.com/biorack/magi
Simka	computes a large collection of standard ecological distances by replacing species counts by k-mer counts	10.7717/peerj-cs.94	https://gatb.inria.fr/software/simka/
Commet	Comparing and combining multiple metagenomic datasets	10.1109/BIBM.2014.6999135	https://colibread.inria.fr/software/commet/
sourmash	Quickly search, compare, and analyze genomic and metagenomic data sets		https://github.com/sourmash-bio/sourmash
p4finder	identify P4-like elements in bacterial genome	10.1098/rstb.2020.0475	https://gitlab.pasteur.fr/jsousa/p4finder
MacSyFinder	Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems	10.1371/journal.pone.0110726	https://github.com/gem-pasteur/macsyfinder
WIsH	Predicting prokaryotic hosts from metagenomic phage contigs	10.1093/bioinformatics/btx383	https://github.com/soedinglab/wish
PPR-Meta	identifying phages and plasmids from metagenomic fragments	10.1093/gigascience/giz066	https://github.com/zhenchengfang/PPR-Meta
Phage_Finder	Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences	10.1093/nar/gkl732	http://phage-finder.sourceforge.net/
iPHoP	host prediction for metagenome-assembled virus genomes	10.1101/2022.07.28.501908	https://bitbucket.org/srouxjgi/iphop
MetaPhage	Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data	10.1128/msystems.00741-22	https://github.com/MattiaPandolfoVR/MetaPhage
Evident	performing effect size and power calculations on microbiome data	10.1101/2022.05.19.492684	https://github.com/biocore/Evident
STATegra	Multi-Omics Data Integration	10.3389/fgene.2021.620453	https://www.bioconductor.org/packages/release/bioc/html/STATegRa.html
wiSDOM	R Shiny interface to conduct analysis and visualization of metagenomic data	10.1093/bioinformatics/btab057	https://github.com/lunching/wiSDOM
MOCHI	cross-platform tool for amplicon-based microbiota analysis	10.1093/bioinformatics/btac494	https://mochi.life.nctu.edu.tw/
EzMAP	Easy Microbiome Analysis Platform	10.1186/s12859-021-04106-7	https://github.com/gnanibioinfo/EzMAP
iCAMP	Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis	10.1038/s41467-020-18560-z	https://github.com/DaliangNing/iCAMP1
BiomeHorizon	Visualizing Microbiome Time Series Data in R	10.1128/msystems.01380-21	https://github.com/blekhmanlab/biomehorizon/
mOTUs3	estimates relative taxonomic abundance of microbial community members using metagenomic shotgun sequencing data	10.1101/2021.04.20.440600	https://github.com/motu-tool/mOTUs
ComplexHeatmap	Complex heatmap visualization	10.1002/imt2.43	https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
mobr	Measurement of Biodiversity (MoB)	10.1111/2041-210X.13102	https://github.com/MoBiodiv/mobr
Meta-Apo	accuracy of 16Samplicon-based prediction of microbiome function	10.1186/s12864-020-07307-1	https://github.com/qibebt-bioinfo/meta-apo
PanACoTA	PANgenome with Annotations, COre identification, Tree and corresponding Alignments	10.1093/nargab/lqaa106	https://github.com/gem-pasteur/PanACoTA
HAYSTAC	robust and rapid species identification in high-throughput sequencing data	10.1371/journal.pcbi.1010493	https://github.com/antonisdim/HAYSTAC
TaxUMAP atlas	Visualize structure in large microbiome datasets	10.1101/2022.09.27.509746	https://github.com/jsevo/taxumap
DeepBIO	biological sequence prediction, functional annotation, and visualization analysis	10.1101/2022.09.29.509859	http://inner.wei-group.net/DeepBIO
BusyBee Web	metagenomic data analysis by bootstrapped supervised binning and annotation	10.1093/nar/gkx348	https://ccb-microbe.cs.uni-saarland.de/busybee
gcMeta	a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data	10.1093/nar/gky1008	https://gcmeta.wdcm.org/
ESPRIT	estimating species richness using large collections of 16S rRNA pyrosequences	10.1093/nar/gkp285	https://biotech.ufl.edu/people/sun/esprit.html
MoRS	Mortality by ribosomal sequencing (MoRS) provides a window into taxon-speciﬁc cell lysis	10.1038/s41396-022-01327-3	https://github.com/kevinzhongxu/tslysis
VEBA	recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	10.1186/s12859-022-04973-8	https://github.com/jolespin/veba
STRONG	resolves strains on assembly graphs		https://github.com/chrisquince/STRONG
biomonitoR	managing ecological data and calculating biomonitoring indices	10.7717/peerj.14183	https://github.com/alexology/biomonitoR
ngsLCA	fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data	10.1111/2041-210X.14006	https://github.com/miwipe/ngsLCA
PHANTASM	PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes	10.1101/2022.10.18.512716	https://github.com/dr-joe-wirth/phantasm
LotuS2	ultrafast and highly accurate tool for amplicon sequencing analysis	10.1186/s40168-022-01365-1	http://lotus2.earlham.ac.uk/
MIntO	Metagenomic and Metatranscriptomic Data Integration	10.3389/fbinf.2022.846922	https://github.com/arumugamlab/MIntO
StrainFacts	Scalable Microbial Strain Inference in Metagenomic Data	10.3389/fbinf.2022.867386	https://github.com/bsmith89/StrainFacts
RecruitPlotEasy	Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity	10.3389/fbinf.2021.826701	https://github.com/KGerhardt/RecruitPlotEasy
Ptools	Pathway Tools Management of Pathway/Genome Data for Microbial Communities	10.3389/fbinf.2022.869150	https://biocyc.org/download.shtml
Graphia	graph-based approach for the visualisation and analysis of bacterial pangenomes	10.1186/s12859-022-04898-2	https://graphia.app/
microTrait	Trait-Based Representation of Microbial Genomes	10.3389/fbinf.2022.918853	https://github.com/ukaraoz/microtrait
16S-ITGDB	Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences	10.3389/fbinf.2022.905489	https://github.com/yphsieh/ItgDB
Metascan	METabolic Analysis, SCreening and ANnotation of Metagenomes	10.3389/fbinf.2022.861505	https://github.com/gcremers/metascan
GoldRush	de novo long read genome assembler with linear time complexity	10.1101/2022.10.25.513734	https://github.com/bcgsc/goldrush
CAMMiQ	Strain level microbial detection and quantification with applications to single cell metagenomics	10.1038/s41467-022-33869-7	https://github.com/algo-cancer/CAMMiQ
Bakta	rapid & standardized annotation of bacterial genomes, MAGs & plasmids	10.1099/mgen.0.000685	https://github.com/oschwengers/bakta
MAGScoT	bin-refinement tool	10.1093/bioinformatics/btac694	https://github.com/ikmb/MAGScoT
BRANEnet	embedding multilayer networks for omics data integration	10.1186/s12859-022-04955-w	https://github.com/Surabhivj/BRANEnet
ResFinderFG v2.0	database of antibiotic resistance genes obtained by functional metagenomics	10.1101/2022.10.19.512667	https://cge.food.dtu.dk/services/ResFinderFG/
MetaNetX	Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks	10.1093/nar/gkaa992	https://www.metanetx.org/
TaxonKit	A Practical and Efficient NCBI Taxonomy Toolkit	10.1016/j.jgg.2021.03.006	https://github.com/shenwei356/taxonkit
CONSULT	contamination removal from genomic sequencing reads	10.1093/nargab/lqab071	https://github.com/noraracht/CONSULT
EukCC	Estimating the quality of eukaryotic genomes recovered from metagenomic analysis	10.1186/s13059-020-02155-4	https://github.com/Finn-Lab/EukCC
CoverM	DNA read coverage and relative abundance calculator focused on metagenomics applications	10.5281/zenodo.10531253	https://github.com/wwood/CoverM
BusyBee	convenient analysis of metagenomic data in the form of assembled contigs or long reads (PacBio or ONT)	10.1093/nar/gkx348	https://ccb-microbe.cs.uni-saarland.de/busybee
ProDeGe	computational protocol for fully automated decontamination of genomes	10.1038/ismej.2015.100
CheckM2	rapid, scalable and accurate tool for assessing microbial genome quality	10.1101/2022.07.11.499243	https://github.com/chklovski/CheckM2
MIDAS2	Metagenomic Intra-species Diversity Analysis System	10.1093/bioinformatics/btac713	https://github.com/czbiohub/MIDAS2
AsgeneDB	Arsenic metabolism gene database and computational tool for metagenome annotation	10.1093/nargab/lqac080	https://github.com/XinweiSong/Asgene
Phage Discovery Guide	Phage Discovery Guide		https://seaphagesphagediscoveryguide.helpdocsonline.com/home
KARGAMobile	Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing	10.3389/fbioe.2022.1016408	https://github.com/Ruiz-HCI-Lab/KargaMobile
genoPlotR	comparative gene and genome visualization in R	10.1093/bioinformatics/btq413	https://genoplotr.r-forge.r-project.org/
Squeegee	De novo identification of microbial contaminants in low microbial biomass microbiomes	10.1038/s41467-022-34409-z	https://gitlab.com/treangenlab/squeegee
Wochenende	modular and flexible alignment-based shotgun metagenome analysis	10.1186/s12864-022-08985-9	https://github.com/MHH-RCUG/nf_wochenende
metaMIC	reference-free misassembly identification and correction of de novo metagenomic assemblies	10.1186/s13059-022-02810-y	https://github.com/ZhaoXM-Lab/metaMIC
HOME	HOst-Microbiota Evolution	10.1111/1755-0998.13063	https://github.com/BPerezLamarque/HOME
RPANDA	R: Phylogenetic ANalyses of DiversificAtion	10.1111/2041-210X.12526	https://github.com/hmorlon/PANDA
RPANDA	measure the phylogenetic signal in a bipartite interaction network	10.1101/2021.08.30.458192	https://github.com/BPerezLamarque/Phylosignal_network
ALE	Reconstruction of reconciled gene trees and estimation of DTL rates from a sample of gene trees and a rooted species tree	10.1093/sysbio/syt054	https://github.com/ssolo/ALE/
vertical transmission	Scripts for running methods to detect vertical transmission	10.1111/1755-0998.13063	https://github.com/BPerezLamarque/Scripts/tree/master/Comparing_methods_vertical_transmission
MEGARes and AMR++	comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification	10.1093/nar/gkac1047	https://www.meglab.org/
metaMIC	reference-free misassembly identification and correction of de novo metagenomic assemblies	10.1186/s13059-022-02810-y	https://github.com/ZhaoXM-Lab/metaMIC
MetaGT	de novo assembly of metatranscriptomes with the aid of metagenomic data	10.3389/fmicb.2022.981458	https://github.com/ablab/metaGT
multi-metagenome	Metagenome assembly guide	10.1038/nbt.2579	https://github.com/MadsAlbertsen/multi-metagenome
mmgenome	extracting individual genomes from metagenomes	10.1101/059121	http://madsalbertsen.github.io/mmgenome/
ampvis2	visualising amplicon data	10.1101/299537	https://github.com/KasperSkytte/ampvis2
MAGE (Microbial Abundance GaugE)	Strain Level Profiling of Metagenome Samples	10.1101/2022.11.24.517382
MaGe (Magnifying Genomes)	microbial genome annotation system supported by synteny results	10.1093/nar/gkj406	https://mage.genoscope.cns.fr/microscope/home/index.php
mi-atlas	interactive and evolving catalog of microbial interactions	10.1093/femsle/fnz125	https://cpauvert.github.io/mi-atlas/
Namco	microbiome explorer	10.1099/mgen.0.000852	https://exbio.wzw.tum.de/namco/
PathSeq	discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic hosts	10.1093/bioinformatics/bty501	https://github.com/broadinstitute/gatk
VIRify	detection, annotation and taxonomic classification pipeline of viruses	10.1371/journal.pcbi.1011422	https://github.com/EBI-Metagenomics/emg-viral-pipeline
proGenomes3	accurately and consistently annotated high-quality prokaryotic genomes	10.1093/nar/gkac1078	https://progenomes.embl.de/
Systems biology slides			https://gitlab.com/principlescellphysiology/teaching-material/-/tree/master/systems_biology
metacoder	parsing, plotting, and manipulating large taxonomic data sets		https://grunwaldlab.github.io/metacoder_documentation/index.html
phyloseq Extensions Index			http://joey711.github.io/phyloseq-extensions/extensions-index.html
The R Graph Gallery			https://r-graph-gallery.com/index.html
RdRp-scan	identify and annotate divergent RNA viruses in metagenomic sequence data	10.1093/ve/veac082	https://github.com/JustineCharon/RdRp-scan/
MetaPredict	predicting metabolic modules in incomplete bacterial genomes	10.1101/2022.12.21.521254	https://github.com/d-mcgrath/MetaPredict
Greengenes2	Greengenes2 phylogeny	10.1101/2022.12.19.520774	https://github.com/biocore/greengenes2
PathIN	visualization of pathway interaction networks	10.1016/j.csbj.2022.12.028	https://pathin.cing-big.hpcf.cyi.ac.cy/
FlashWeave	predict ecological interactions between microbes from large-scale compositional abundance data	10.1016/j.cels.2019.08.002	https://github.com/meringlab/FlashWeave.jl
Victors	a web-based knowledge base of virulence factors in human and animal pathogens	10.1093/nar/gky999	http://www.phidias.us/victors
KEMET	python tool for KEGG Module evaluation and microbial genome annotation expansion	10.1016/j.csbj.2022.03.015	https://github.com/Matteopaluh/KEMET
MeRRCI	Metagenome, Resistome, and Replicome for Causal Inferencing	10.1099/mgen.0.000899	https://github.com/stebliankin/merrci
Bacterial Genetics Course Packet	Course packets for Bacterial Genetics and Physiology		https://github.com/graymicrolab/Bacterial_Genetics_Course_Packet
Tools for Microbiome Analysis	A list of R environment based tools for microbiome data exploration, statistical analysis and visualization		https://microsud.github.io/Tools-Microbiome-Analysis/
SprayNPray	user-friendly taxonomic profiling of genome and metagenome contigs	10.1186/s12864-022-08382-2	https://github.com/Arkadiy-Garber/SprayNPray
OpenGenomeBrowser	web platform for genome data management and comparative genomics	10.1186/s12864-022-09086-3	https://opengenomebrowser.github.io/
MicNet toolbox	Visualizing and unraveling a microbial network	10.1371/journal.pone.0259756	https://github.com/Labevo/MicNetToolbox
MetaBinner	binning method to recover individual genomes from complex microbial communities	10.1186/s13059-022-02832-6	https://github.com/ziyewang/MetaBinner
gget	Efficient querying of genomic reference databases	10.1093/bioinformatics/btac836	https://github.com/pachterlab/gget
FastViromeExplorer-Novel	Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data	10.1089/cmb.2022.0397	https://github.com/saima-tithi/FVE-novel
PhyloPlus	Phylogenetic Interrogation of Metagenomic Communities	10.1128/mbio.03455-22	https://github.com/Dennis-xyHuang/PhyloPlus
skani	Fast and robust metagenomic sequence comparison through sparse chaining	10.1101/2023.01.18.524587	https://github.com/bluenote-1577/skani
EasyAmplicon	pipeline for amplicon data analysis	10.1002/imt2.83	https://github.com/YongxinLiu/EasyAmplicon
PhyloPic	Free silhouette images of animals, plants, and other life forms		http://phylopic.org/
VTAM	pipeline for validating metabarcoding data using controls	10.1016/j.csbj.2023.01.034	https://github.com/aitgon/vtam
ViWrap	identify, bin, classify, and predict viral-host relationships for viruses from metagenomes	10.1101/2023.01.30.526317	https://github.com/AnantharamanLab/ViWrap
BIRDMAn	robust inference of host-microbe associations	10.1101/2023.01.30.526328	https://github.com/biocore/BIRDMAn
Snippy	Rapid haploid variant calling and core genome alignment		https://github.com/tseemann/snippy
REALPHY	Reference sequence Alignment based Phylogeny builder	10.1093/molbev/msu088	https://realphy.unibas.ch/realphy/
stRainy	assembly-based metagenomic strain phasing using long reads	10.1038/s41592-024-02424-1	https://github.com/katerinakazantseva/stRainy
FuncDiv	computation of contributional diversity metrics from microbiome data	10.1093/bioinformatics/btac809	https://github.com/gavinmdouglas/FuncDiv
InStrain	analysis of co-occurring genome populations from metagenomes	10.1038/s41587-020-00797-0	https://github.com/MrOlm/instrain
gcplyr	import, wrangle, and do model-free analyses of microbial growth curve data		https://mikeblazanin.github.io/gcplyr/
Symbiont-screener	reference-free tool to separate host sequences from symbionts for error-prone long reads	10.3389/fmars.2023.1087447	https://github.com/BGI-Qingdao/Symbiont-Screener
DeepBIO	platform for high-throughput biological sequence prediction, functional annotation and visualization analysis	10.1093/nar/gkad055	https://inner.wei-group.net/DeepBIO/
gutSMASH	predict specialized primary metabolic pathways from the human gut microbiota	10.1038/s41587-023-01675-1	https://github.com/victoriapascal/gutsmash/tree/gutsmash
VirBot	RNA viral contig detector for metagenomic data	10.1093/bioinformatics/btad093	https://github.com/GreyGuoweiChen/RNA_virus_detector
BinaRena	dedicated interactive platform for human-guided exploration and binning of metagenomes	10.1101/2022.06.28.498025	https://github.com/qiyunlab/binarena
StrainSelect	novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide	10.1016/j.heliyon.2023.e13314	http://strainselect.secondgenome.com
MGnify Genomes	biome-specific microbial genome catalogues	10.1016/j.jmb.2023.168016	https://www.ebi.ac.uk/metagenomics/browse/genomes/
kb_DRAM	Annotating and functional profiling of genomes with DRAM in KBase	10.1093/bioinformatics/btad110	https://github.com/shafferm/kb_DRAM
GT-Pro	ultra-rapid genotyping of prokaryotes in shotgun metagenomes	10.1038/s41587-021-01102-3	https://github.com/zjshi/gt-pro
Maast	microbial agile accurate SNP typing	10.1101/2022.07.06.499075	https://github.com/zjshi/Maast
Bactabolize	high-throughput genome-scale metabolic reconstruction and growth simulation pipeline	10.1101/2023.02.26.530115	https://github.com/kelwyres/Bactabolize
MetaPhlAn 4	Metagenomic Phylogenetic Analysis	10.1038/s41587-023-01688-w	https://github.com/biobakery/MetaPhlAn
Bacteriophages playing nice	gut bacteria-phage interactions	10.1016/j.isci.2023.106007	https://github.com/sgsutcliffe/Bacteriophages_Playing_Nice
BlobToolKit	Interactive Quality Assessment of Genome Assemblies	10.1534/g3.119.400908	https://blobtoolkit.genomehubs.org/
perfect bacterial genome	Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing	10.1371/journal.pcbi.1010905	https://github.com/rrwick/Perfect-bacterial-genome-tutorial
inStrain	profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	10.1038/s41587-020-00797-0	https://github.com/MrOlm/inStrain
fastq-dl	Download FASTQ files from the European Nucleotide Archive or the Sequence Read Archive repositories		https://github.com/rpetit3/fastq-dl
SatelliteFinder	Detection of four families of phage satellites: P4-like, PICI, cfPICI and PLE in protein datasets	10.1093/nar/gkad123	https://hub.docker.com/r/gempasteur/satellite_finder
SnakeMAGs	workflow to reconstruct prokaryotic genomes from metagenomes	10.12688/f1000research.128091.1	https://github.com/Nachida08/SnakeMAGs
geNomad	classification and annotation framework to identify sequences of plasmids and viruses	10.1101/2023.03.05.531206	https://portal.nersc.gov/genomad
dragonflye	Assemble bacterial isolate genomes from Nanopore reads		https://github.com/rpetit3/dragonflye
hybracter	Hybrid (and long-only) bacterial assembly pipeline	10.1099/mgen.0.001244	https://github.com/gbouras13/hybracter
Trycycler	generating consensus long-read assemblies for bacterial genomes	10.1186/s13059-021-02483-z	https://github.com/rrwick/Trycycler
plassembler	Automated Bacterial Plasmid Assembly Program	10.1093/bioinformatics/btad409	https://github.com/gbouras13/plassembler
PhaGAA	integrated web server platform for phage genome annotation and analysis	10.1093/bioinformatics/btad120	phage.xialab.info
eOmics	an R package for improved omics data analysis	10.1101/2023.03.11.532240	https://github.com/yuabrahamliu/eOmics
compare_genomes	a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes	10.1101/2023.03.16.533049	https://github.com/jeffersonfparil/compare_genomes
SCRuB	Source tracking for Contamination Removal in microBiomes	10.1038/s41587-023-01696-w	https://github.com/Shenhav-and-Korem-labs/SCRuB
demografr	Approximate Bayesian Computation (ABC) toolkit for R		https://github.com/bodkan/demografr
MetaErg	Metagenome Annotation Pipeline		https://xiaoli-dong.github.io/metaerg/
plastiC	pipeline for recovery and characterization of plastid genomes from metagenomic datasets	10.12688/wellcomeopenres.19589.2	https://github.com/Finn-Lab/plastiC
r-statistics co	educational resource for computing in R		http://r-statistics.co/
Phenonaut	toolkit for multi-omic phenotypic space exploration	10.1093/bioinformatics/btad143	https://github.com/CarragherLab/phenonaut
KARGVA	K-mer antibiotic resistance gene variant analyzer	10.3389/fmicb.2023.1060891	https://github.com/DataIntellSystLab/KARGVA
KARGA	K-mer-based Antibiotic Resistance Gene (ARG) Analysis of High-Throughput Sequencing Data	10.1109/BHI50953.2021.9508479	https://github.com/DataIntellSystLab/KARGA
Secmarker	Computational identification of the selenocysteine tRNA (tRNASec) in genomes	10.1371/journal.pcbi.1005383	https://secmarker.crg.es/
MicrobeCensus	estimate average genome size from shotgun metagenomic data	10.1186/s13059-015-0611-7	https://github.com/snayfach/MicrobeCensus
metasssnake2	snakemake/python based metagenomics pipeline		https://github.com/moritzbuck/0053_metasssnake2
MetAnnotate	function-specific taxonomic profiling and comparison of metagenomes	10.1186/s12915-015-0195-4	https://github.com/MetAnnotate/MetAnnotate
UProC	tools for ultra-fast protein domain classification	10.1093/bioinformatics/btu843	https://github.com/gobics/uproc
mi-faser	microbiome - functional annotation of sequencing reads	10.1093/nar/gkx1209	https://bitbucket.org/bromberglab/mifaser/src/master/
fusionDB	assessing microbial diversity and environmental preferences via functional similarity networks	10.1093/nar/gkx1060	https://services.bromberglab.org/fusiondb/
fusion	functional-repertoire similarity-based organism network	10.1371/journal.pcbi.1004472	https://bromberglab.org/?q=services
Predict-Protein	predicting secondary structure and returning families of related proteins		https://bitbucket.org/bromberglab/predictprotein/src/master/
fuNTRp	creating functional maps of protein sequences		https://bitbucket.org/bromberglab/funtrp/src/master/
pEffect	predicts bacterial type III effector proteins		https://services.bromberglab.org/peffect/
Herodotools	An R package to integrate macroevolution, biogeography and community ecology	10.1111/jbi.14610	https://github.com/GabrielNakamura/Herodotools
Ensemble Quotient Optimization (mEQO) for microbiome	Annotation-free discovery of functional groups in microbial communities	10.1038/s41559-023-02021-z	https://github.com/Xiaoyu2425/mEQO
ViroProfiler	viral metagenomic data analysis	10.1080/19490976.2023.2192522	https://github.com/deng-lab/viroprofiler
PanKmer	k-mer based and reference-free pangenome analysis	10.1101/2023.03.31.535143	https://gitlab.com/salk-tm/pankmer
PanGraphViewer	A Versatile Tool to Visualize Pangenome Graphs	10.1101/2023.03.30.534931	https://github.com/TF-Chan-Lab/panGraphViewer
UMAP	Uniform Manifold Approximation and Projection for Dimension Reduction	10.48550/arXiv.1802.03426	https://github.com/lmcinnes/umap
AMON	annotation of metabolite origins via networks to integrate microbiome and metabolome data	10.1186/s12859-019-3176-8	https://github.com/lozuponelab/AMON
GenoVi	automated circular genome visualizer for bacteria and archaea	10.1371/journal.pcbi.1010998	https://github.com/robotoD/GenoVi
Phables	from fragmented assemblies to high-quality bacteriophage genomes	10.1093/bioinformatics/btad586	https://github.com/Vini2/phables
PanGenome Graph Builder (PGGB)	Building pangenome graphs	10.1101/2023.04.05.535718	https://github.com/pangenome/pggb
ClassGraph	Improving Metagenomic Read Classification with Overlap Graphs	10.1089/cmb.2022.0208	https://github.com/MargheritaCavattoni/ClassGraph
SUPER-FOCUS	agile functional analysis of metagenomic data	10.1093/bioinformatics/btv584	https://github.com/metageni/SUPER-FOCUS
PLASS	Protein-Level ASSembler		https://github.com/soedinglab/plass
MGX	management and analysis of metagenomic datasets	10.1186/s40168-018-0460-1	https://mgx-metagenomics.github.io/
MGX 2.0	Shotgun- and assembly-based metagenome and metatranscriptome analysis from a single source	10.1101/2023.09.21.558800	https://mgx-metagenomics.github.io
LookingGlass	deep learning model for read-length biological sequences	10.1038/s41467-022-30070-8	https://github.com/ahoarfrost/LookingGlass/
fastBio	manipulating data and creating and training deep learning models for biological sequencing data	10.1038/s41467-022-30070-8	https://github.com/ahoarfrost/fastBio/
ShortBRED	High-Specificity Targeted Functional Profiling in Microbial Communities	10.1371/journal.pcbi.1004557	https://huttenhower.sph.harvard.edu/shortbred/
transXpress	streamlined de novo transcriptome assembly and annotation	10.1186/s12859-023-05254-8	https://github.com/transXpress/transXpress
microbial-genes	gene catalog of 17 different microbial ecosystems	10.1128/msystems.00118-23	https://www.microbial-genes.bio/
MJOLNIR	Metabarcoding Joining Obitools & Linkage Networks In R		https://github.com/uit-metabarcoding/MJOLNIR
MJOLNIR3	Metabarcoding Joining Obitools & Linkage Networks In R		https://github.com/adriantich/MJOLNIR3
EvoMIL	Prediction of virus-host association	10.1101/2023.04.07.536023	https://github.com/liudan111/EvoMIL
CyanoSeq	a database of cyanobacterial 16S rRNA sequences with curated taxonomy	10.1111/jpy.13335	https://zenodo.org/record/7569105
GALBA	Genome Annotation with Miniprot and AUGUSTUS	10.1101/2023.04.10.536199	https://github.com/Gaius-Augustus/GALBA
THAPBI PICT	fast, cautious, and accurate metabarcoding analysis pipeline	10.1101/2023.03.24.534090	https://github.com/peterjc/thapbi-pict/
AmphoraNet	webserver implementation of the AMPHORA2 metagenomic workflow suite	10.1016/j.gene.2013.10.015	http://amphoranet.pitgroup.org
AMPHORA2	An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences	10.1093/bioinformatics/bts079	https://github.com/wu-lab-uva/AMPHORA2
Phyla_AMPHORA	A Phylum-specific Automated Phylogenomic Inference Pipeline for Bacterial Sequences	10.1093/molbev/mst059	https://github.com/wu-lab-uva/Phyla_AMPHORA
YAMP	containerized workflow enabling reproducibility in metagenomics research	10.1093/gigascience/giy072	https://github.com/alesssia/YAMP
Metagenome-Atlas	a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data	10.1186/s12859-020-03585-4	https://github.com/metagenome-atlas/atlas
cogeqc	assess genome assembly and annotation quality, orthogroup inference, and synteny detection	10.1101/2023.04.14.536860	https://github.com/almeidasilvaf/cogeqc
UGMAGrefiner	increase completeness and resolution of metagenome-assembled genomes	10.1016/j.csbj.2023.03.030
BarcoSim	simulates DNA barcode sequences		https://github.com/loukesio/barcosim
Making maps with R			https://www.paulamoraga.com/tutorial-maps/
CORRAL	identification of eukaryotes in shotgun metagenomic data	10.1186/s40168-023-01505-1	github.com/wbazant/CORRAL
cblindplot	create colour blind friendly plots	10.1016/j.ecoinf.2023.102045	https://github.com/ducciorocchini/cblindplot
PopCOGenT	Identifying microbial populations using networks of horizontal gene transfer	10.1016/j.cell.2019.06.033	https://github.com/philarevalo/PopCOGenT
SAVEMONEY	Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing	10.1101/2023.04.12.536413	https://github.com/MasaakiU/MultiplexNanopore
microshades	custom color shading palettes that improve accessibility and data organization		https://github.com/KarstensLab/microshades
YACHT	an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample	10.1093/bioinformatics/btae047	https://github.com/KoslickiLab/YACHT
LucaProt	A novel deep learning framework that incorporates protein amino acid sequence and structure information to predict protein function	10.1101/2023.04.18.537342	https://github.com/alibaba/LucaProt
rtrees	an R package to assemble phylogenetic trees from megatrees	10.1111/ecog.06643	https://github.com/daijiang/rtrees
U.PhyloMaker	An R package that can generate large phylogenetic trees for plants and animals	10.1016/j.pld.2022.12.007	https://github.com/jinyizju/U.PhyloMaker
HOTSPOT	Hierarchical hOst predicTion for aSsembled Plasmid cOntigs with Transformer	10.1093/bioinformatics/btad283	https://github.com/Orin-beep/HOTSPOT
Recentrifuge	Robust comparative analysis and contamination removal for metagenomics	10.1371/journal.pcbi.1006967	https://github.com/khyox/recentrifuge
hkgfinder	Find housekeeping genes in prokaryotic (meta)genomes		https://github.com/Ebedthan/hkgfinder
Conditional Quantile Regression (ConQuR)	a comprehensive microbiome batch effects removal tool	10.1038/s41467-022-33071-9	https://github.com/wdl2459/ConQuR
ggpicrust2	an R package for PICRUSt2 predicted functional profile analysis and visualization	arXiv:2303.10388	https://github.com/cafferychen777/ggpicrust2
Read2Tree	Inference of phylogenetic trees directly from raw sequencing reads	10.1038/s41587-023-01753-4	https://github.com/DessimozLab/read2tree
Calculation of the Percentage Of Conserved Proteins (POCP)	proposed genus boundary for the prokaryotes based on genomic insights	10.1128/JB.01688-14	https://github.com/hoelzer/pocp
MetQuest	identifying all possible pathways from metabolic networks between the source and the target metabolites	10.1038/s41598-018-28007-7	https://github.com/RamanLab/metquest2
Residual neural network for Misassembled Contig identification (ResMiCo)	Increasing the quality of metagenome-assembled genomes with deep learning	10.1371/journal.pcbi.1011001	https://github.com/leylabmpi/ResMiCo
KOunt	calculating KEGG orthologue abundance in metagenomic sequence data	10.1101/2023.04.27.538265	https://github.com/WatsonLab/KOunt
TOGA	Tool to infer Orthologs from Genome Alignments	10.1126/science.abn3107	https://github.com/hillerlab/TOGA
GUNC	detection of chimerism and contamination in prokaryotic genomes	10.1186/s13059-021-02393-0	https://github.com/grp-bork/gunc
SoilTemp	A global database of near-surface temperature	10.1111/gcb.15123	https://www.soiltempproject.com/
BacterAI	automated science platform that maps microbial metabolism but requires no prior knowledge	10.1038/s41564-023-01376-0	https://github.com/jensenlab/BacterAI
Proksee	in-depth characterization and visualization of bacterial genomes	10.1093/nar/gkad326	https://proksee.ca/
Genomes on a Tree (GoaT)	search engine for genomic and sequencing project metadata across the eukaryotic tree of life	10.12688/wellcomeopenres.18658.1	https://goat.genomehubs.org/
pvogs_function	predicting functional associations between pVOGs	10.1186/s12859-021-04343-w	https://github.com/MGXlab/pvogs_function
phap	Phage Host Analysis Pipeline		https://github.com/MGXlab/phap
CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT)	10.1186/s13059-019-1817-x	https://github.com/MGXlab/CAT
Social Niche Breadth (SNB)	A social niche breadth score reveals niche range strategies of generalists and specialists	10.1038/s41559-023-02027-7	https://github.com/MGXlab/social_niche_breadth_SNB
nf-core/eager	best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data	10.7717/peerj.10947	https://github.com/nf-core/eager
PHASTEST	PHAge Search Tool with Enhanced Sequence Translation	10.1093/nar/gkad382	https://phastest.ca/
clusterProfiler	enrichment tool for interpreting omics data	10.1016/j.xinn.2021.100141	https://github.com/YuLab-SMU/clusterProfiler
DePolymerase Predictor (DePP)	targeted identification of phage depolymerases	10.1186/s12859-023-05341-w	https://github.com/DamianJM/Depolymerase-Predictor
GIL	python package for designing custom indexing primers	10.1093/bioinformatics/btad328	https://github.com/de-Boer-Lab/GIL
VirPipe	pipeline for detecting viral genomes from Nanopore sequencing	10.1093/bioinformatics/btad293	https://github.com/KijinKims/VirPipe
WebQUAST	online evaluation of genome assemblies	10.1093/nar/gkad406	https://www.ccb.uni-saarland.de/quast
gRodon	an R package to estimate maximal growth rates of prokaryotes	10.1073/pnas.2016810118	https://github.com/jlw-ecoevo/gRodon2
gRodon2	an R package to estimate maximal growth rates of microbial eukaryotes	10.1101/2021.10.15.464604	https://github.com/jlw-ecoevo/gRodon2
Metagenome Mode v2	Community-Wide Estimates of Growth Potential from Metagenomes	10.1128/msystems.00745-22	https://github.com/jlw-ecoevo/gRodon2
Growth Rate InDex (GRiD)	estimating in situ growth rates of ultra-low coverage (>0.2×) and de novo-assembled metagenomes	10.1038/s41467-018-07240-8	https://github.com/ohlab/GRiD
Strain-level Metagenomic Estimation of Growth rate (SMEG)	measures growth rates of bacterial subspecies or strains from complex metagenomic samples	10.1126/sciadv.aaz2299	https://github.com/ohlab/SMEG
Pest Alert Tool	a web-based application for flagging species of concern in metabarcoding datasets	10.1093/nar/gkad364	https://pest-alert-tool-prod.azurewebsites.net/
CRABS	Creating Reference databases for Amplicon-Based Sequencing	10.1111/1755-0998.13741	https://github.com/gjeunen/reference_database_creator
itol.toolkit	working with iTOL (Interactive Tree Of Life) by an automated generation of annotation files	10.1093/bioinformatics/btad339	https://github.com/TongZhou2017/itol.toolkit
Genekitr	R package and a corresponding web server to assist exploring large gene sets	10.1186/s12859-023-05342-9	https://github.com/GangLiLab/genekitr
microbiomeExplorer	analyze and visualize microbial community sequencing data		https://github.com/zoecastillo/microbiomeExplorer
Anansi	Knowledge-based Integration of Multi-Omic Datasets	10.48550/arXiv.2305.10832	https://github.com/thomazbastiaanssen/anansi
Pygenomics	manipulating genomic intervals and data files in Python	10.1093/bioinformatics/btad346	https://gitlab.com/gtamazian/pygenomics
Phanta	Rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes	10.1038/s41587-023-01799-4	https://github.com/bhattlab/phanta
Minigraph-Cactus	combine multiple reference genome assemblies into a pangenome reference graph	10.1038/s41587-023-01828-2	https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md
MgCod	Gene Prediction in Phage Genomes with Multiple Genetic Codes	10.1016/j.jmb.2023.168159	https://github.com/gatech-genemark/MgCod
miaSim	an R/Bioconductor package to easily simulate microbial community dynamics	10.1111/2041-210X.14129	https://github.com/microbiome/miaSim
FALCON	analysis of nestedness in bipartite network	10.12688/f1000research.4831.1	https://github.com/sjbeckett/FALCON
Arcadia-Science/metagenomics	pipeline for profiling metagenomes obtained through either Illumina or Nanopore technologies		https://github.com/Arcadia-Science/metagenomics
Py2R	code translator tool from Python to R or from R to Python		https://github.com/ianandersonlol/Py2R
DAS Tool	calculate an optimized, non-redundant set of bins from a single assembly	10.1038/s41564-018-0171-1	https://github.com/cmks/DAS_Tool
Bacterial Wars (BW)	prediction of bacterial predominance based on network analysis measures	10.1093/nargab/lqad049	https://bioinformatics.cing.ac.cy/bacterialwars
Contig Overlap Based Re-Assembly (COBRA)	get higher quality virus genomes assembled from short-read metagenomes	10.1101/2023.05.30.542503	https://github.com/linxingchen/cobra.github.io
rCRUX	Generating Metabarcoding Reference libraries in R	10.1101/2023.05.31.543005	https://github.com/CalCOFI/rCRUX
Metabuli	metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences	10.1101/2023.05.31.543018	https://github.com/steineggerlab/Metabuli
iTaxoTools	specimen-based software toolkit for taxonomists	10.11646/MEGATAXA.6.2.1	https://github.com/iTaxoTools
U-CIE	Color encoding of high-dimensional data	10.1002/pro.4388	https://github.com/mikelkou/ucie
kmindex	indexing and querying sequencing samples		https://github.com/tlemane/kmindex
miniBUSCO	a faster and more accurate reimplementation of BUSCO	10.1101/2023.06.03.543588	https://github.com/huangnengCSU/minibusco
CViewer	integration of shotgun metagenomics with other omics datasets	10.1101/2023.06.07.544017	https://github.com/KociOrges/cviewer
SPIKEPIPE	accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes	10.1111/1755-0998.13057	https://github.com/dougwyu/ArcDyn
CAMAMED	composition-aware mapping-based analysis of metagenomic data	10.1093/nargab/lqaa107	https://github.com/mhnb/camamed
Sunbeam	pipeline for analyzing metagenomic sequencing experiments	10.1186/s40168-019-0658-x	https://github.com/sunbeam-labs/sunbeam
ViWrap	identify, bin, classify, and predict viral–host relationships for viruses from metagenomes	10.1002/imt2.118	https://github.com/AnantharamanLab/ViWrap
BRAKER3	Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence	10.1101/2023.06.10.544449	https://hub.docker.com/r/teambraker/braker3
pyGenomeViz	genome visualization python package for comparative genomics		https://pypi.org/project/pygenomeviz/
clinker	Gene cluster comparison figure generator	10.1093/bioinformatics/btab007	https://github.com/gamcil/clinker
BGCFlow	Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets	10.1101/2023.06.14.545018	https://github.com/NBChub/bgcflow
mPTP	Species delimitation using the multi-rate Poisson Tree Processes	10.1093/bioinformatics/btx025	https://github.com/Pas-Kapli/mptp
ASAP	assemble species by automatic partitioning	10.1111/1755-0998.13281	https://bioinfo.mnhn.fr/abi/public/asap/
odp	Oxford Dot Plots or Ancient gene linkages (ALG)-genome comparisons	10.1038/s41586-023-05936-6	https://github.com/conchoecia/odp
GenAlEx	population genetic analysis	10.1093/bioinformatics/bts460	https://biology-assets.anu.edu.au/GenAlEx/Welcome.html
Bamboozle	identification and quantification of intraspecific barcodes	10.1101/2023.03.16.532925	https://github.com/topel-research-group/Bamboozle
MultiTax	Python package to obtain, parse and explore biological taxonomies		https://github.com/pirovc/multitax
euka	detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs	10.1101/2023.04.04.535531	https://github.com/grenaud/vgan
Reconstructor	COBRApy-compatible tool that produces high-quality draft reconstructions	10.1093/bioinformatics/btad367	https://github.com/emmamglass/reconstructor
metaDMG	Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data	10.1101/2022.12.06.519264	https://github.com/metaDMG-dev
Bakdrive	identifying a minimum set of bacterial species driving interactions across multiple microbial communities	10.1093/bioinformatics/btad236	https://gitlab.com/treangenlab/bakdrive
Hecatomb	‘sacrifice’ false-positive viral reads from metagenomes to enrich for true-positive viral reads	10.1101/2022.05.15.492003	https://github.com/shandley/hecatomb
Phynteny	Synteny-based annotation of bacteriophage genes		https://github.com/susiegriggo/Phynteny
CALOUR	exploratory and interactive microbiome analysis based on heatmaps	10.1128/msystems.00269-18	https://github.com/amnona/calour
pangene	construct a pangenome gene graph		https://github.com/lh3/pangene
Phyloformer	towards fast and accurate phylogeny estimation with self-attention networks	10.1101/2022.06.24.496975	https://github.com/lucanest/Phyloformer
AmpliDiff	An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes	10.1101/2023.07.22.550164	https://github.com/JaspervB-tud/AmpliDiff
Greengenes2	Greengenes2 unifies microbial data in a single reference tree	10.1038/s41587-023-01845-1	https://greengenes2.ucsd.edu/
uDANCE	Updating phylogenetic and phylogenomic trees using divide and conquer		https://github.com/balabanmetin/uDance
The LifeMonitor GitHub app	application of workflow sustainability best practices		https://crs4.github.io/life_monitor/lm_wft_best_practices_github_app
MetaCerberus	HMM-based implementation for robust functional annotation across the tree of life	10.1101/2023.08.10.552700	https://github.com/raw-lab/metacerberus
ggvolc	translates differential expression datasets and RNAseq data into informative volcano plots		https://github.com/loukesio/ggvolc
GEN-ERA toolbox	comparative genomics of bacteria and small eukaryotes	10.1093/gigascience/giad022	https://github.com/Lcornet/GENERA
MultiQC	Aggregate results from bioinformatics analyses across many samples into a single report	10.1093/bioinformatics/btw354	https://github.com/ewels/MultiQC
CRACOT	CRitical Assessment of genomic COntamination detection at several Taxonomic ranks	10.1101/2022.11.14.516442	https://github.com/Lcornet/GENERA/wiki/20.-CRACOT
ORPER (ORganism PlacER)	A Workflow for Constrained SSU rRNA Phylogenies	10.3390/genes12111741	https://github.com/Lcornet/ORPER
ToRQuEMaDA	tool for retrieving queried Eubacteria, metadata and dereplicating assemblies	10.7717/peerj.11348	https://bitbucket.org/phylogeno/tqmd/src/master/
BinaRena	interactive platform for human-guided exploration and binning of metagenomes	10.1186/s40168-023-01625-8	https://github.com/qiyunlab/binarena
DeGenPrime	robust primer design and optimization	10.1101/2023.08.11.553048	https://github.com/raw-lab/DeGenPrime
KOunt	a reproducible KEGG orthologue abundance workflow	10.1093/bioinformatics/btad483	https://github.com/WatsonLab/KOunt
iModulonDB	a knowledgebase of microbial transcriptional regulation derived from machine learning	10.1093/nar/gkaa810	https://imodulondb.org/
DataHarmonizer	data harmonization, validation, aggregation and analysis of pathogen genomics	10.1099/mgen.0.000908	https://github.com/cidgoh/DataHarmonizer
ggCaller	Accurate and fast graph-based pangenome annotation and clustering	10.1101/gr.277733.123	https://github.com/samhorsfield96/ggCaller
snpless-nf	time-course analysis with bacterial NGS whole-genome data		https://github.com/kullrich/snpless-nf
metagenome-based virus-to-microbe ratio (VMR) estimate (mVRM)	Metagenome-derived virus-microbe ratios	10.1038/s41396-023-01431-y	https://gitlab.com/anagtz/mvmrs
THAPBI PICT	a fast, cautious, and accurate metabarcoding analysis pipeline	10.7717/peerj.15648	https://github.com/peterjc/thapbi-pict/
SemiBin2	self-supervised contrastive learning leads to better MAGs	10.1093/bioinformatics/btad209	https://github.com/BigDataBiology/SemiBin/
MetaDecoder	clustering metagenomic contigs	10.1186/s40168-022-01237-8	https://github.com/liu-congcong/MetaDecoder/
MArVD2	a machine learning enhanced tool to discriminate between archaeal and bacterial viruses	10.1038/s43705-023-00295-9	https://bitbucket.org/MAVERICLab/marvd2/src/master/
‘SRS’ R Package	Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)	10.3390/app112311473	https://github.com/vitorheidrich/SRS_q2-srs_info
BugSigDB	a database for identifying unusual abundance patterns in human microbiome studies	10.1038/s41587-023-01872-y	https://github.com/waldronlab/BugSigDB
MVP	Modular Viromics Pipeline	10.1128/msystems.00888-24	https://gitlab.com/ccoclet/mvp
Mycotools	An Automated and Scalable Platform for Comparative Genomics	10.1101/2023.09.08.556886	https://github.com/xonq/mycotools
Orchestrating Microbiome Analysis (OMA) with Bioconductor			https://microbiome.github.io/OMA/index.html
Effective microbial richness (EMR)		10.1038/s43705-021-00033-z	https://zenodo.org/record/4837436
Strain Genome Explorer (StrainGE)	toolkit to track and characterize low-abundance strains in complex microbial communities	10.1186/s13059-022-02630-0	https://github.com/broadinstitute/strainge
cpnDB	chaperonin database		https://www.cpndb.ca/
PopPUNK	Fast and flexible bacterial genomic epidemiology	10.1101/gr.241455.118	https://github.com/bacpop/PopPUNK
euka	tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA	10.1111/2041-210X.14214	https://github.com/grenaud/vgan
compleasm	faster and more accurate reimplementation of BUSCO	10.1093/bioinformatics/btad595	https://github.com/huangnengCSU/compleasm
ANCOM-BC	Analysis of Compositions of Microbiomes with Bias Correction	10.1038/s41467-020-17041-7	https://github.com/FrederickHuangLin/ANCOM-BC-Code-Archive
BLCA	Bayesian-based LCA taxonomic classification method	10.1186/s12859-017-1670-4	https://github.com/qunfengdong/BLCA
FAST (Feature-Assisted Segmenter/Tracker)	Tracking bacteria at high density	10.1371/journal.pcbi.1011524	https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php
AleRax	gene and species tree co-estimation and reconciliation	10.1101/2023.10.06.561091	https://github.com/BenoitMorel/AleRax
Qmatey	automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes	10.1093/bib/bbad351	https://github.com/bodeolukolu/Qmatey
MetADAta MicrobiomE (MADAME)	user-friendly bioinformatic tool for data and metadata retrieval in microbiome research	10.1101/2023.10.14.562335	https://github.com/BiomeResearchTeam/MADAME
VIRUSBreakend	identifies viral DNA presence and genomic integration	10.1093/bioinformatics/btab343	https://github.com/PapenfussLab/VIRUSBreakend
Spae	Phage toolkit to detect phage candidates for phage therapy		https://github.com/linsalrob/spae
pimba	PIpeline for MetaBarcoding Analysis which allows the use of customized databases, as well as other reference databases	10.1007/978-3-030-91814-9_10	https://github.com/reinator/pimba
BIRDS	Biodiversity Information Review and Decision Support package for R		https://greenswayab.github.io/BIRDS/index.html
CodiMD	collaborate in real-time with markdown		https://github.com/hackmdio/codimd
Protist_barcode_MAG_correspondence	integrate information between metabarcoding and metagenomic datasets and explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent	10.1101/2023.10.09.561583	https://github.com/beaplab/Protist_barcode_MAG_correspondence
nf-core/taxprofiler	metagenomic taxonomic classification and profiling	10.1101/2023.10.20.563221	https://github.com/nf-core/taxprofiler
SOCfinder	genomic tool for identifying cooperative genes in bacteria	10.1099/mgen.0.001171	https://github.com/lauriebelch/SOCfinder
BarKeeper	web framework to assemble, analyze and manage DNA barcode data and metadata	10.1111/2041-210X.14047	https://github.com/DNA-BarKeeper/barkeeper , http://barkeeper.uni-muenster.de/
RasperGade16S	Prediction and correction of 16S rRNA Gene Copy Numners (GCN)	10.1038/s43705-023-00266-0	https://github.com/wu-lab-uva/RasperGade16S
RasperGade	Reconstructing Ancestral State under Pulsed Evolution in R by Gaussian Decomposition	10.1093/sysbio/syac016	https://github.com/wu-lab-uva/RasperGade
BacArena	Modeling Framework for Cellular Communities in their Environments	10.1371/journal.pcbi.1005544	https://bacarena.github.io/
SPIRE	Searchable, Planetary-scale mIcrobiome REsource	10.1093/nar/gkad943	https://spire.embl.de/
Geometric viability assay (GVA)	high-throughput and low-waste viability assay for microbes	10.1038/s41564-023-01513-9	https://www.colorado.edu/lab/chatterjeelab/geometric-viability-assay-gva
ggrepel	Avoid overlapping text labels in graphs		https://github.com/slowkow/ggrepel
Environmentally-Driven Edge Detection Program (EnDED)	Disentangling environmental effects in microbial association networks	10.1186/s40168-021-01141-7	https://github.com/InaMariaDeutschmann/EnDED
Extended local similarity analysis (eLSA)	network construction	10.1101/2021.07.13.452187	https://github.com/InaMariaDeutschmann/TemporalNetworkBBMO
Extended local similarity analysis (eLSA)	extends LSA to time series data with replicates	10.1186/1752-0509-5-S2-S15	http://meta.usc.edu/softs/lsa
Seasonal niche differentiation among closely related marine bacteria		10.1038/s41396-021-01053-2	https://github.com/adriaaulaICM/bbmo_niche_sea
benchdamic	benchmarking of differential abundance method for microbiome data	10.1093/bioinformatics/btac778	https://bioconductor.org/packages/release/bioc/html/benchdamic.html
LMAS (Last Metagenomic Assembler Standing)	evaluating metagenomic short de novo assembly methods through defined communities	10.1093/gigascience/giac122	https://github.com/B-UMMI/LMAS
ALDEx2 (ANOVA-Like Differential Expression tool)	Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account	10.1186/2049-2618-2-15	https://www.bioconductor.org/packages/release/bioc/html/ALDEx2.html
zCompositions	Imputation of Zeros, Nondetects and Missing Data in Compositional Data Sets	10.1016/j.chemolab.2015.02.019	https://github.com/cran/zCompositions
robCompositions	Compositional Data Analysis	10.1002/9781119976462.ch25	https://cran.r-project.org/web/packages/robCompositions/index.html
WebVOWL	Web-based Visualization of Ontologies	10.3233/SW-150200	http://vowl.visualdataweb.org/webvowl.html
StrainPanDA	A strain analysis pipeline based on pangenome	10.1002/imt2.41	https://github.com/xbiome/StrainPanDA
SpaceMicrobe	detect microbial reads in 10X Visium Spatial Gene Expression data		https://github.com/bedapub/space-microbe
splicekit	splicing analysis from short-read RNA-seq	10.1101/2023.05.25.542256	https://github.com/bedapub/splicekit
Besca	single-cell transcriptomics analysis toolkit	10.1093/nargab/lqab102	https://bedapub.github.io/besca/
SCALA	multimodal analysis of single-cell Next Generation Sequencing data	10.1016/j.csbj.2023.10.032	https://scala.fleming.gr
AMDirT	AncientMetagenomeDir Toolkit	10.12688/f1000research.134798.1	https://github.com/SPAAM-community/AMDirT
AncientMetagenomeDir	community curated resource of lists of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples and libraries		https://github.com/SPAAM-community/AncientMetagenomeDir
Provenance Replay	Facilitating bioinformatics reproducibility	10.1371/journal.pcbi.1011676	https://github.com/qiime2/provenance-lib
IAS Hotspot Model	running species distribution models for marine species		https://github.com/biomobst/IAS_hotspot_model
EMODnetWFS	Access EMODnet Web Feature Service data through R		https://github.com/EMODnet/EMODnetWFS
EMODnetWCS	interrogation of and access to EMODnet geographic raster data in R though the EMODnet Web Coverage Services		https://github.com/EMODnet/EMODnetWCS
Btrait	facilitates working with species density data, combined with species traits		https://github.com/EMODnet/Btrait
comspat	analyze within-community spatial organization using species combinations	10.1111/ecog.06216	https://github.com/jamestsakalos/comspat
MultiBarcodeTools	Easy selection of optimal primers for eDNA multi-metabarcoding	10.1002/edn3.499	https://multibarcode.k.u-tokyo.ac.jp/
MAGqual	standalone pipeline to assess the quality of metagenome-assembled genomes	10.1101/2023.12.13.571510	https://github.com/ac1513/MAGqual
Predicted Relative Metabolomic Turnover (PRMT)	determining metabolic turnover	10.1186/2042-5783-1-4
MMINP	A computational framework of microbemetabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm	10.1080/19490976.2023.2223349	https://github.com/YuLab-SMU/MMINP
METAGENassist	user-friendly, web-based analytical pipeline for comparative metagenomic studies	10.1093/nar/gks497	http://www.metagenassist.ca/METAGENassist/faces/Home.jsp
plotgardener	genomic data visualization package for R	10.1093/bioinformatics/btac057	https://github.com/PhanstielLab/plotgardener
g(r)osling	build interactive genomics visualizations with Gosling		https://github.com/gosling-lang/grosling
ggcoverage	visualize and annotate genome coverage for various NGS data	10.1186/s12859-023-05438-2	https://github.com/showteeth/ggcoverage
App-SpaM	Alignment-free phylogenetic placement algorithm based on Spaced-word Matches	10.1101/2020.10.19.344986	https://github.com/matthiasblanke/App-SpaM
MicroNiche	assessing microbial niche breadth and overlap from amplicon sequencing data	10.1093/femsec/fiaa131	https://cran.r-project.org/web/packages/MicroNiche/index.html
MIMt	A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification	10.1101/2023.12.15.571851	https://mimt.bu.biopolis.pt/
metabaR	r package for the evaluation and improvement of DNA metabarcoding data quality	10.1111/2041-210X.13552	https://github.com/metabaRfactory/metabaR
argNorm	Antibiotic resistance gene (ARG) normalization by mapping to the antibiotic resistance ontology (ARO) by CARD	10.5204/rep.eprints.252448	https://github.com/BigDataBiology/argNorm
stratfreshDB	Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds	10.1038/s41597-021-00910-1	https://figshare.scilifelab.se/articles/dataset/StratFreshDB_v1_0/13005311/2
STAMPS 2019 wiki			https://github.com/mblstamps/stamps2019/wiki
POGENOM	determine allele frequencies in the metagenomes and calculate π and FST values	10.1038/s41396-021-00985-z	https://github.com/EnvGen/POGENOM
Population-structure	Contains scripts used in the study “Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria”	10.1101/2023.07.13.548520	https://github.com/thr44pw00d/population-structure
Coracle	a machine learning framework to identify bacteria associated with continuous variables	10.1093/bioinformatics/btad749	http://www.micportal.org/coracle/index/
GSR-DB	a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis	10.1128/msystems.00950-23	https://manichanh.vhir.org/gsrdb/
multiSMASH	A workflow and scripts for large-scale antiSMASH analyses	10.5281/zenodo.8276143	https://github.com/zreitz/multismash/
pangenome_rf	Pangenome analysis using random forests	10.1073/pnas.2304934120	https://github.com/alanbeavan/pangenome_rf
BactInt	domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text	10.1016/j.compbiolchem.2023.108012
happi	a hierarchical approach to pangenomics inference	10.1186/s13059-023-03040-6	https://github.com/statdivlab/happi
VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis)	primers and optimized protocol for eukaryotic endosymbiont metabarcoding	10.1038/s41467-023-44521-3
microTrait	Trait-Based Representation of Microbial Genomes	10.3389/fbinf.2022.918853	https://github.com/ukaraoz/microtrait
Metagenomic Thermometer	predicting environmental temperature based on metagenomic sequences	10.1093/dnares/dsad024	http://palaeo.nig.ac.jp/metathermo
Tome	prediction of optimal growth temperature of microorganisms and enzyme catalytic optima		https://github.com/EngqvistLab/Tome
CNN_tRNA_OGT	tRNA thermometer to estimate microbial adaptation to temperature	10.1093/nar/gkaa1030	https://bitbucket.org/bucklerlab/cnn_trna_ogt/src/master/
ASTRAL	genome-scale coalescent-based species tree estimation	10.1093/bioinformatics/btu462	https://github.com/smirarab/ASTRAL/
ASTRAL-III	polynomial time species tree reconstruction from partially resolved gene trees	10.1186/s12859-018-2129-y	https://github.com/smirarab/ASTRAL
AleRax	species & gene tree co-estimation and reconciliation	10.1101/2023.10.06.561091	https://github.com/BenoitMorel/AleRax
GeneRax	Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss	10.1093/molbev/msaa141	https://github.com/BenoitMorel/GeneRax
SpeciesRax	Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss	10.1093/molbev/msab365	https://github.com/BenoitMorel/GeneRax
Asteroid	infer species trees from gene trees under high proportions of missing data	10.1093/bioinformatics/btac832	https://github.com/BenoitMorel/Asteroid
ALE	generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies	10.1093/bioinformatics/bts723	http://www.alescore.org
AnnoView	large-scale analysis, comparison, and visualization of microbial gene neighborhoods	10.1101/2024.01.15.575735	http://annoview.uwaterloo.ca/annoview/
KAUST Metagenomic Analysis Platform (KMAP)	analyse (browse, query, compare) annotated metagenomic datasets	10.3389/fsci.2023.1038696	http://www.cbrc.kaust.edu.sa/kmap/index.php
phydms	phylogenetic analyses using deep mutational scanning data to inform the substitution models	10.7717/peerj.3657	https://jbloomlab.github.io/phydms/
Friends Don’t Let Friends Make Bad Graphs	opinionated essay about good and bad practices in data visualization	10.5281/zenodo.7542491	https://github.com/cxli233/FriendsDontLetFriends
animalcules	R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny	10.1186/s40168-021-01013-0	https://github.com/wejlab/animalcules
eDITH	an R-package to spatially project eDNA-based biodiversity across river networks	10.1101/2024.01.16.575835	https://github.com/lucarraro/test_eDITH
edgeR 4.0	powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets	10.1101/2024.01.21.576131	https://bioinf.wehi.edu.au/edgeR/
NNforge	Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences	10.1101/2024.01.26.576649	https://gitlab.com/oveoyas/nnforge
DeepGOMeta	Predicting functions for microbes	10.1101/2024.01.28.577602	https://github.com/bio-ontology-research-group/deepgometa
SingleM	profiling shotgun metagenomes using conserved regions within universal marker genes	10.1101/2024.01.30.578060	https://wwood.github.io/singlem/
Sandpiper	interrogating public shotgun metagenome datasets, presenting the results generated by SingleM	10.1101/2024.01.30.578060	https://sandpiper.qut.edu.au
Smafa	A read aligner for aligned sequences		https://github.com/wwood/smafa
TEPI	Taxonomy-aware Embedding and Pseudo-Imaging for Scarcely-labeled Zero-shot Genome Classification	10.48550/arXiv.2401.13219
FEEDS (Food wastE biopEptiDe claSsifier)	biopeptide prediction and classification tool	10.1016/j.crbiot.2024.100186	https://github.com/vborincenturion/feeds
ClustVis	a web tool for visualizing clustering of multivariate data	10.1093/nar/gkv468	https://biit.cs.ut.ee/clustvis/
ReMIND	A constraint-based framework to reconstruct interaction networks in microbial communities	10.1101/2024.01.30.577913	https://github.com/EPFL-LCSB/remind
mkLTG	taxonomic assignment of metabarcoding sequences using variable identity thresholds	10.1007/s42977-024-00201-x	https://github.com/meglecz/mkLTG
COInr and mkCOInr	Building and customizing a nonredundant barcoding reference database from BOLD and NCBI	10.1111/1755-0998.13756	https://github.com/meglecz/mkCOInr
BASTA (BAsic Sequence Taxonomy Annotation)	Taxonomic classification of sequences and sequence bins using last common ancestor estimations	10.1111/2041-210X.13095	https://github.com/timkahlke/BASTA
GenomeFace	a deep learning-based metagenome binner	10.1101/2024.02.07.579326
microbeMASST	a taxonomically informed mass spectrometry search tool for microbial metabolomics data	10.1038/s41564-023-01575-9	https://github.com/robinschmid/microbe_masst
Dashing Growth Curves	web application for rapid and interactive analysis of microbial growth curves	10.1186/s12859-024-05692-y	https://dashing-growth-curves.ethz.ch/
mbctools	Metabarcoding and Cross-Platform Pipeline	10.1101/2024.02.08.579441	https://github.com/GuilhemSempere/mbctools
PIMENTA	PIpeline for MEtabarcoding through Nanopore Technology used for Authentication	10.1101/2024.02.14.580249	https://github.com/WFSRDataScience/PIMENTA
Mg-Traits pipeline	advancing functional trait-based approaches in metagenomics	10.3897/aca.4.e64908	https://github.com/pereiramemo/metagenomic_pipelines
Environmentally-Driven Edge Detection Program (EnDED)	Disentangling environmental effects in microbial association networks	10.1186/s40168-021-01141-7	https://github.com/InaMariaDeutschmann/EnDED
rshift	paleoecology and regime shift analysis		https://github.com/alexhroom/rshift
Placement Evaluation WOrkflows (PEWO)	a collection of workflows to benchmark phylogenetic placement	10.1093/bioinformatics/btaa657	https://github.com/phylo42/PEWO
EPIK	precise and scalable evolutionary placement with informative k-mers	10.1093/bioinformatics/btad692	https://github.com/phylo42/EPIK
PhylteR	Efficient Identification of Outlier Sequences in Phylogenomic Datasets	10.1093/molbev/msad234	https://github.com/damiendevienne/phylter
SpacerPlacer	reconstructing ancestral CRISPR spacer arrays along a given phylogenetic tree	10.1101/2024.02.20.581079	https://github.com/fbaumdicker/SpacerPlacer
PIGMENTUM	an easy pigment-based tool for monitoring phytoplankton community composition	10.3354/meps14518
dbBact	community knowledge base for information about mircobial ecology	10.1093/nar/gkad527	https://www.dbbact.org/main
ProkFunFind	detect genes of functional interest	10.1128/msystems.00036-24	https://github.com/nlm-irp-jianglab/ProkFunFind
phyloMDA	an R package for phylogeny-aware microbiome data analysis	10.1186/s12859-022-04744-5	https://github.com/liudoubletian/phyloMDA
sandbox.bio	Interactive bioinformatics tutorials		https://sandbox.bio/
awesome-r-dataviz	Curated resources for Data Visualization, Drawing & Publishing in R		https://krzjoa.github.io/awesome-r-dataviz
RAWGraphs	A free and open source tool for data visualization		https://www.rawgraphs.io/
TICI	a taxon-independent community index for eDNA-based ecological health assessment	10.7717/peerj.16963	https://zenodo.org/records/10396304
Microbiota data analysis			https://scienceparkstudygroup.github.io/microbiome-lesson/
microViz	R package for analysis and visualization of microbiome sequencing data	10.21105/joss.03201	https://david-barnett.github.io/microViz/index.html
MicrobiomeStat	Supporting Longitudinal Microbiome Analysis in R		https://www.microbiomestat.wiki/
GToTree	a user-friendly workflow for phylogenomics	10.1093/bioinformatics/btz188	https://github.com/AstrobioMike/GToTree
Web of Microbes (WoM)	a curated microbial exometabolomics database for linking chemistry and microbes	10.1186/s12866-018-1256-y	https://metatlas.nersc.gov/wom/project-begin.view
GenomeSPOT	Predicting microbial growth conditions from amino acid composition	10.1101/2024.03.22.586313	https://github.com/cultivarium/GenomeSPOT
Kioloa PopGen	SNP-Based population genomics		https://green-striped-gecko.github.io/kioloa/
srahunter	A User-Friendly Tool for Efficient Retrieval and Management of SRA Data	10.1101/2024.03.19.585745	https://socket.dev/pypi/package/srahunter
Basestack	platform for rapid and real time analysis of Nanopore generated sequencing data		https://github.com/jhuapl-bio/Basestack
anpan	consolidate statistical methods for strain analysis		https://github.com/biobakery/anpan
MACARRoN	Metabolome Analysis and Combined Annotation Ranks to pRioritize Novel bioactives		https://huttenhower.sph.harvard.edu/macarron/
WAAFLE	identifying LGTs from community metagenomes		https://huttenhower.sph.harvard.edu/waafle
specificity	an R package for analysis of feature specificity	10.1186/s40793-022-00426-0	https://github.com/darcyj/specificity
FAIR training handbook			https://elixir-europe-training.github.io/ELIXIR-TrP-FAIR-training-handbook/
EXPLANA	EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies	10.1101/2024.03.20.585968	https://github.com/JTFouquier/explana
ORCA	Predicting replication origins in circular prokaryotic chromosomes	10.1101/2024.03.28.587133	https://github.com/ZoyavanMeel/ORCA
hAMRonization	Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling	10.1101/2024.03.07.583950	https://github.com/pha4ge/hAMRonization
QMD	quantify microbial absolute abundance differences between groups	10.1002/imt2.78	https://github.com/Xingyinliu-Lab/QMD/tree/master
PLASS	Protein-Level ASSembler	10.1038/s41592-019-0437-4	https://github.com/soedinglab/plass
PenguiN	Protein guided nucleotide assembler	10.1101/2024.03.29.587318	https://github.com/soedinglab/plass
LRBinner	Binning Error-Prone Long Reads Using Auto Encoders	10.1186/s13015-022-00221-z	https://github.com/anuradhawick/LRBinner
MGnify-LR WorkflowMGnify-Long Read Workflow		https://github.com/KateSakharova/mgnify-lr
R-package Tutorial			https://github.com/loukesio/R-package-tutorial
BASALT	refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis	10.1038/s41467-024-46539-7	https://github.com/EMBL-PKU/BASALT
CyanoCyc	cyanobacterial web portal	10.3389/fmicb.2024.1340413	https://cyanocyc.org/
Predictive Ecosystem Analyzer (PEcAn)	Develop and promote accessible tools for reproducible ecosystem modeling and forecasting		https://pecanproject.github.io/
slow5curl	Streamlining remote nanopore data access	10.1093/gigascience/giae016	https://github.com/BonsonW/slow5curl
Resistance Gene Association and Inference Network (ReGAIN)	Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens	10.1101/2024.02.26.582197	https://github.com/ERBringHorvath/regain_cl
OlinkRPackage	versatile toolbox to enable easy and smooth handling of Olink NPX data to speed up your proteomic research		https://github.com/Olink-Proteomics/OlinkRPackage
radEmu	R package for estimating changes in the abundance of microbial taxa	10.48550/arXiv.2402.05231	https://github.com/statdivlab/radEmu
QuickVariants	Fast and Accurate Variant Identification Tool for Sequencing-Based Studies	10.1186/s12915-024-01891-4	https://github.com/caozhichongchong/QuickVariants
Functional resemblance	A new look at functional beta diversity	10.1101/2024.02.25.580632
The ASV registry	The ASV registry is part of the project GBOL III	10.3897/arphapreprints.e125475	https://asv.bolgermany.de/metabarcoding
GSMc	Global Soil Mycobiome consortium dataset	10.1007/s13225-021-00493-7	https://github.com/Mycology-Microbiology-Center/GSMc
happi	Hierarchical Approach to Pangenomics Inference	10.1186/s13059-023-03040-6	https://github.com/statdivlab/happi
breakaway	premier package for statistical analysis of microbial diversit		https://github.com/adw96/breakaway
Gene tRee Ordination Visualization for ExplorationS (groves)	R package for visualizing a set of gene-level phylogenies	10.1093/biostatistics/kxad025	https://github.com/statdivlab/groves
Count Regression for Correlated Observations with the Beta-binomial (corncob)	R package for modeling relative abundance and testing hypotheses about the effect of covariates on relative abundance	10.1214/19-AOAS1283	https://github.com/statdivlab/corncob
tinyvamp	package for estimation and removal of measurement error in high-throughput sequencing data	10.48550/arXiv.2204.12733	https://github.com/statdivlab/tinyvamp
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations (paramedic)	R package for estimating microbial concentration	10.1111/biom.13503	https://github.com/statdivlab/paramedic
Regression, Inference, and General Data Analysis Tools for R (rigr)	R package to streamline data analysis in R		https://github.com/statdivlab/rigr
global microbial smORF catalogue (GMSC)	integrated, consistently-processed, smORFs catalogue of the microbial world	10.1101/2023.12.27.573469	https://gmsc.big-data-biology.org/home
BIOlogical ocean data reforMATting Effort (BIO-MATE)	reformats openly sourced published datasets from oceanographic voyages	10.1038/s41597-024-03038-0	https://github.com/KimBaldry/BIOMATE-Rpackage
MicrobioSee	A Web-Based Visualization Toolkit for Multi-Omics of Microbiology	10.3389/fgene.2022.853612	https://microbiosee.gxu.edu.cn
Snekmer	scalable pipeline for protein sequence fingerprinting based on amino acid recoding	10.1093/bioadv/vbad005	https://github.com/PNNL-CompBio/Snekmer
DataHarmonizer	A standardized browser-based spreadsheet editor and validator that can be run offline and locally	10.1099/mgen.0.000908	https://github.com/cidgoh/DataHarmonizer
National Microbiome Data Collaborative (NMDC) Schema	FAIR microbiome data sharing network		https://github.com/microbiomedata/nmdc-schema
ZooTraits	R shiny app for exploring animal trait data for ecological and evolutionary research	10.1002/ece3.11334	https://github.com/thiago-goncalves-souza/zootraits
NORMAN ARB&ARG	NORMAN Antibiotic Resistant Bacteria and Resistance Genes Database	10.1016/j.watres.2024.121689	https://www.norman-network.com/nds/bacteria/
metaVaR	MetaVariant Species (MVS) for reference-free and metagenomic-based population genomic analysis	10.1371/journal.pone.0244637	https://github.com/madoui/metaVaR
Microbe Atlas Project	Explore the microbiome of the world		https://microbeatlas.org/
MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis	10.1093/bioinformatics/btx517	https://github.com/jfmrod/mapseq
World Ocean Database (WOD)			https://www.ncei.noaa.gov/products/world-ocean-database
Ocean Climate Laboratory Team (OCL)			https://www.ncei.noaa.gov/products/ocean-climate-laboratory
Microbiome Analysis Pipeline (LCPM)	comprehensive pipeline for analyzing microbiome data from the LCMP cohort	10.1038/s41591-024-02963-2	https://github.com/raeslab/QMP-Microbiome-CRC-confounders/
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT)	taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs / bins)	10.1186/s13059-019-1817-x	https://github.com/MGXlab/CAT_pack
Read Annotation Tool (RAT)	estimates the taxonomic composition of metagenomes using CAT and BAT output	10.1038/s41467-024-47155-1	https://github.com/MGXlab/CAT_pack
Viral Eukaryotic Bacterial Archaeal (VEBA)	modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics	10.1101/2024.03.08.583560	https://github.com/jolespin/veba
microgeo	an R package rapidly displays the biogeographic traits of soil microbial communities on maps	10.1093/femsec/fiae087	https://github.com/ChaonanLi/microgeo
tidyomics	enhancing omic data analyses	10.1038/s41592-024-02299-2	https://github.com/tidyomics
Gut Microbiome Health Index (GMHI)	A predictive index for health status using species-level gut microbiome profiling	10.1038/s41467-020-18476-8	https://github.com/jaeyunsung/GMHI_2020
GMWI-webtool	a user-friendly browser application for assessing health through metagenomic gut microbiome profiling	10.1093/bioinformatics/btad061	https://gmwi-webtool.github.io/
microHI (microbiota health index)	health index of the environmental microbiota to predict the health status of aquatic wildlife	10.1016/j.ecolind.2023.110346
Distance to Reference Communities Index (DRCI)	tool to assess communities’ restoration success	10.1111/rec.14194
Ocean Barcode Atlas	a web service to explore the biodiversity and biogeography of marine organisms	10.1111/1755-0998.13322	https://oba.mio.osupytheas.fr/ocean-atlas/
QuPath	Open Software for Bioimage Analysis	10.1038/s41598-017-17204-5	https://qupath.github.io
MANOCCA (Multivariate Analysis of Conditional CovAriance)	test for the effect of a predictor on the covariance matrix of a multivariate outcome	10.1101/2023.09.20.558234	https://gitlab.pasteur.fr/statistical-genetics/manocca
nf-core/nanoseq	Nanopore demultiplexing, QC and alignment pipeline	10.1038/s41587-020-0439-x	https://nf-co.re/nanoseq/3.1.0
ONTbarcoder 2.0	rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4	10.1111/cla.12566	https://github.com/asrivathsan/ONTbarcoder
SeMPI	a genome-based secondary metabolite prediction and identification web server	10.1093/nar/gkx289	https://www.pharmaceutical-bioinformatics.de/SeMPI/
Thanos	An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples	10.3390/microorganisms12071264	https://github.com/zhezhaozoe/thanos
Shiny app	Put your Shiny app on the web by using your own servers or Posit’s hosting service		https://shiny.posit.co/
gargammel	a sequence simulator for ancient DNA	10.1093/bioinformatics/btw670	https://grenaud.github.io/gargammel/
MALT	alignment of metagenomic reads against a database of reference sequences	10.1038/s41559-017-0446-6	https://software-ab.cs.uni-tuebingen.de/download/malt/welcome.html
SNPEvaluation	a tool allowing for evaluating and visualizing confidence in variant calling of low-coverage pathogen genomes	10.1073/pnas.1820447116	https://github.com/andreasKroepelin/SNP_Evaluation
MaltExtract-Interactive Plotting App (MEx-IPA) tool	interactive viewer of output from the HOPS metagenomic authentication pipeline	10.5281/zenodo.3380011	https://zenodo.org/records/4771942
EAGER	scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data	10.1186/s13059-016-0918-z	https://github.com/apeltzer/EAGER-GUI
nf-core/eager	Reproducible, portable, and efficient ancient genome reconstruction	10.7717/peerj.10947	https://github.com/nf-core/eager
cuperdec	R package to generate ‘Cumulative Percent Decay’ curves, with optional filtering functions, for microbial taxonomic profiles	10.1073/pnas.2021655118	https://github.com/jfy133/cuperdec
DamageProfiler	calculate damage profiles of mapped ancient DNA reads	10.1093/bioinformatics/btab190	https://github.com/Integrative-Transcriptomics/DamageProfiler
metaBIT	integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data	10.1111/1755-0998.12546	https://bitbucket.org/Glouvel/metabit/src/master/
CoproID	predicts the source of coprolites and paleofeces using microbiome composition and host DNA content	10.7717/peerj.9001	https://github.com/nf-core/coproid
FEAST	fast expectation-maximization for microbial source tracking	10.1038/s41592-019-0431-x	https://github.com/cozygene/FEAST
HOPS	automated detection and authentication of pathogen DNA in archaeological remains	10.1186/s13059-019-1903-0	https://github.com/rhuebler/HOPS
Holi	pipeline for taxonomic profiling of ancient metagenomic reads based on competitive mapping to large databases	10.1038/nature19085	https://github.com/ancient-eDNA/Holi
BacDiveR	R package provides a programmatic interface to the Bacterial Diversity Metadatabase of the DSMZ		https://github.com/TIBHannover/BacDiveR
Metapresence	accurate species detection in metagenomics based on the genome-wide distribution of mapping reads	10.1128/msystems.00213-24	https://github.com/davidesangui/metapresence
fqlink	retrieve ENA fastq links from NCBI accession codes		https://github.com/TTTPOB/fqlink
Global Change Analysis Model (GCAM)	integrated assessment tool for exploring consequences and responses to global change	10.5194/gmd-12-677-2019	https://github.com/JGCRI/gcam-core
Global Biosphere Management Model (GLOBIOM)	A global model to assess competition for land use between agriculture, bioenergy, and forestry		https://globiom.org/
DisBalance	a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data	10.1093/bib/bbab094	https://github.com/yangfenglong/DisBalance
Microbiome data science with R/Bioconductor			https://microbiome.github.io/course_2022_radboud/
gcplyr	import, wrangle, and do model-free analyses of microbial growth curve data	10.1186/s12859-024-05817-3	https://mikeblazanin.github.io/gcplyr/
Ocean Monitoring Indicators (OMI)	free downloadable trends and datasets covering the past quarter of a century		https://marine.copernicus.eu/access-data/ocean-monitoring-indicators
GLMMs for the Microbiome	Applying generalized linear mixed models (GLMMs) to wild metabarcoding data	10.1128/msystems.00040-23	https://arsweeny.github.io/microbiome-glmm/
Island biogeography theory and the gut microbiome		10.1093/ismejo/wrae114	https://github.com/Gibbons-Lab/IBT-and-the-Gut-Microbiome
Shiny-phyloseq	interactive web application that provides a graphical user interface to the phyloseq	10.1093/bioinformatics/btu616	https://joey711.github.io/shiny-phyloseq/
phold	Phage Annotation using Protein Structures	10.1101/2025.08.05.668817	https://github.com/gbouras13/phold
Prophage-DB	a database of prophages, their proteins, and associated metadata	10.1101/2024.07.11.603044	https://github.com/AnantharamanLab/Prophage-DB
mettannotator	a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies	10.1093/bioinformatics/btaf037	https://github.com/EBI-Metagenomics/mettannotator
SRA-Explorer	Mini web application to explore the NCBI Sequence Read Archive and easily access downloads for data		https://github.com/ewels/sra-explorer
Biodiversity of Marine Planktonic Copepods	Thesaurus (from the cited literature from 1883 to 2019)		https://copepodes.obs-banyuls.fr/en/
Phylo-tree_eDNA	create phylogenetic trees based on taxonomic assignments of Environmental DNA (eDNA) data		https://github.com/Enorya/Phylo-tree_eDNA
RiboGrove tools	a database of full-length prokaryotic 16S rRNA genes derived from completely assembled genomes	10.1016/j.resmic.2022.103936	https://github.com/masikol/ribogrove-tools
HiOrCo	Computing Higher-Order Co-occurrence patterns in microbial samples		https://github.com/cdanielmachado/HiOrCo
Dbfetch	Dbfetch provides an easy way to retrieve entries from various databases at the EMBL-EBI in a consistent manneρ	10.1093/nar/gkac240	https://www.ebi.ac.uk/Tools/dbfetch/
SNIPe	Selecting Novel Informative Primer-sets for e-DNA	10.1002/edn3.590	https://snipe.dlougheed.com
pipecraft	a Graphical User Interface (GUI) software that implements various popular tools for metabarcoding data analyses		https://github.com/pipecraft2/pipecraft
SURPI (Sequence-Based Ultra-Rapid Pathogen Identification)	pathogen identification from complex metagenomic next-generation sequencing (NGS) data	10.1101/gr.171934.113	https://github.com/chiulab/surpi/tree/master
CLARK	Fast, accurate and versatile sequence classification system	10.1186/s12864-015-1419-2	http://clark.cs.ucr.edu/
GOTTCHA (Genomic Origin Through Taxonomic CHAllenge)	Accurate read-based metagenome characterization using a hierarchical suite of unique signatures	10.1093/nar/gkv180	https://lanl-bioinformatics.github.io/GOTTCHA/
NanoGalaxy	Nanopore long-read sequencing data analysis in Galaxy	10.1093/gigascience/giaa105	https://nanopore.usegalaxy.eu
ASaiM	a Galaxy-based framework to analyze microbiota data	10.1093/gigascience/giy057	https://github.com/ASaiM/framework
MetaPro	a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities	10.1186/s40168-023-01562-6	https://github.com/ParkinsonLab/MetaPro
NanoForms	an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes	10.7717/peerj.13056	https://nanoforms.tech/home/
MicrobiomePhylo	Metabarcoding Data Downstream Analysis	10.1101/2024.04.08.588598	https://microbiomephylo.com
lsaBGC-Pan	mine the pan-BGC-ome of a microbial taxon for biosynthetic golden nuggets	10.1099/mgen.0.000988	https://github.com/Kalan-Lab/lsaBGC-Pan
MICROPHERRET	MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques	10.1186/s40793-024-00600-6	https://github.com/BizzoTL/MICROPHERRET/
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)	Fast and flexible bacterial genomic epidemiology	10.1101/gr.241455.118	https://github.com/bacpop/PopPUNK
PopPIPE (Population analysis PIPEline)	Downstream analysis of PopPUNK results. Produces subclusters and visualisations of all strains		https://github.com/bacpop/PopPIPE
ggCaller	Accurate and fast graph-based pangenome annotation and clustering	10.1101/2023.01.24.524926	https://github.com/bacpop/ggCaller
BacQuerya	search engine for genomic metadata for bacterial pathogens		https://github.com/bacpop/BacQuerya
mandrake	Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding	10.1098/rstb.2021.0237	https://github.com/bacpop/mandrake
unitig-caller	Determines presence/absence of sequence elements in bacterial sequence data	10.1101/695338	https://github.com/bacpop/unitig-caller
pyseer	a comprehensive tool for microbial pangenome-wide association studies	10.1093/bioinformatics/bty539	https://github.com/mgalardini/pyseer
CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs)	automatically generate pangenomes from metagenome assembled genomes	10.1093/bioinformatics/btae542	https://github.com/bacpop/CELEBRIMBOR
panaroo	A Bacterial Pangenome Analysis Pipeline		https://github.com/gtonkinhill/panaroo
Intermediate Research Programming Course			https://iprogramming.bacpop.org/
GlobDB genomes database	a dereplicated set of species representative microbial genomes		https://globdb.org/
SMETANA (species metabolic interaction analysis)	describe the potential for cross-feeding interactions between community members	10.1073/pnas.1421834112	https://github.com/cdanielmachado/smetana
VITCOMIC2	visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing	10.1186/s12918-018-0545-2	http://vitcomic.org/
The Microbe Directory (TMD)	database of microbial features and ecological characteristics		https://themicrobedirectory.shinyapps.io/website/
LEA (Latent Environment Allocation of microbial community data)	evaluate typicality and heterogeneity of microbial communities	10.1371/journal.pcbi.1006143	http://leamicrobe.jp/
metaGEM	reconstruction of genome scale metabolic models directly from metagenomes	10.1093/nar/gkab815	https://github.com/franciscozorrilla/metaGEM
NEMETEX (NEtwork for METabolic EXchanges)	graphical visualizations of metabolite exchanges within complex communities	10.1101/2022.10.19.492777	https://github.com/palakela/NEMETEX
coidb	A small python package for downloading and processing metabarcoding references		https://github.com/biodiversitydata-se/coidb
ARETE (Antimicrobial Resistance: Emergence, Transmission, and Ecology)	pipeline for profiling the genomic repertoire and evolutionary dynamics of microorganisms with a particular focus on pathogens	10.1099/mgen.0.000880	https://github.com/beiko-lab/arete
PHORCE (Phage-Host Observation for Rate estimation from Collapse Events)	phage amplification rates and phage-antibiotic interactions	10.1101/2024.06.07.597930
MicroEcoTools	Theoretical Microbial Ecology Computational Tools	10.1101/2024.08.19.608598	https://www.github.com/Soheil-A-Neshat/MicroEcoTools
Chronospaces	statistical exploration of divergence times	10.1111/2041-210X.14404	https://github.com/mongiardino/chronospace
FASTGA	Fast Genome Aligner		https://github.com/thegenemyers/FASTGA
binchicken	targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly		https://github.com/AroneyS/binchicken
SEPP (SATé-Enabled Phylogenetic Placement)	phylogenetic placement of short reads into reference alignments and trees		https://github.com/smirarab/sepp/tree/master
TIPP (Taxonomic Identification and Phylogenetic Profiling)	a modification of SEPP for classifying query sequences (i.e. reads) using phylogenetic placement	10.1093/bioinformatics/btu721	https://github.com/TeraTrees/TIPP/
plateplanner	Design Beautiful Platemaps		https://plateplanner.nitro.bio/
miaverse	R/Bioconductor framework for microbiome data science		https://microbiome.github.io/
metabaRpipe	an R package to process raw metabarcoding data into a phyloseq object using a single command		https://github.com/fconstancias/metabaRpipe/
Microbial Abundances Retrieved from Sequencing data—automated NCBI Taxonomy (MARS)	processing of metagenomic datasets, taxonomic name resolution, and mapping to resources	10.1093/bioadv/vbae068	https://github.com/ThieleLab/mars-pipeline ; https://mars-pipeline.streamlit.app/along
GlobTherm	global database on thermal tolerances for aquatic and terrestrial organisms	10.1038/sdata.2018.22	https://datadryad.org/stash/dataset/doi:10.5061/dryad.1cv08
BOLD v4	A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data	10.1007/978-1-0716-3581-0_26	https://v4.boldsystems.org
DENSE (DE Novo emerged gene SEarch)	detection of taxonomically restricted genes (TRGs) through phylostratigraphy, and filtering of TRGs for de novo emerged genes via genome comparisons and synteny search	10.1093/gbe/evae159	https://github.com/i2bc/dense
Big Fantastic Virus Database (BFVD)	repository of predicted viral protein structures	10.1101/2024.09.08.611582	https://bfvd.steineggerlab.workers.dev
MagicLamp	toolkit for annotation of genomic data using discreet and curated HMM sets		https://github.com/Arkadiy-Garber/MagicLamp
SprayNPray	Rapid and simple taxonomic profiling of genome and metagenome contigs	10.1186/s12864-022-08382-2	https://github.com/Arkadiy-Garber/SprayNPray
tombRaider	improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion	10.1101/2024.08.23.609468	https://github.com/gjeunen/tombRaider_R
SVbyEye	visual tool to characterize structural variation among whole genome assemblies	10.1101/2024.09.11.612418	https://github.com/daewoooo/SVbyEye
Fungtion	A Server for Predicting and Visualizing Fungal Effector Proteins	10.1016/j.jmb.2024.168613	https://step3.erc.monash.edu/Fungtion/
GDPF	distribution of prokaryotic protein families across the global biosphere	10.1093/nar/gkad869	http://bioinfo.qd.sdu.edu.cn/GDPF/
NAMERS	a purpose-built reference DNA sequence database to support applied eDNA metabarcoding	10.1101/2023.10.06.561210	https://namers.ca/
rix	Reproducible Data Science Environments with ‘Nix’	10.32614/CRAN.package.rix	https://github.com/ropensci/rix
SIAMCAT	pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes	10.1186/s13059-021-02306-1	https://siamcat.embl.de/
MrIML 2.0	Multivariate (multi-response) interpretable machine learning	10.22541/au.172676147.77148600/v1	https://nfj1380.github.io/mrIML/index.html
WoRMS-functional-groups	access and format functional group data for marine species		https://github.com/tomjwebb/WoRMS-functional-groups
OceanOmics-amplicon-nf	Pipeline to analyse amplicon data from raw reads to ecologically informative phyloseq objects		https://github.com/MinderooFoundation/OceanOmics-amplicon-nf
CODARFE (COmpositional Data Anlises with Recursive Feature Elimination)	sparse compositional microbiome-predictors selection and prediction of continuous environmental factors	10.1101/2024.07.18.604052	https://github.com/alerpaschoal/CODARFE
Domestic Feral Cat Metagenomics	Functional insights into the effect of feralisation on the gut microbiota of cats worldwide	10.1101/2024.09.04.611329	https://alberdilab.github.io/domestic_feral_cat_metagenomics/
EasyMicrobiomeR	The best practice for microbiome analysis using R	10.1093/procel/pwad024	https://github.com/taowenmicro/EasyMicrobiomeR
GECCO	Biosynthetic Gene Cluster prediction with Conditional Random Fields	10.1101/2021.05.03.442509	https://gecco.embl.de/
A-microbiologist-wants-to-compute			https://github.com/SvetlanaUP/A-microbiologist-wants-to-compute
Wekemo Bioincloud	platform for meta‐omics data analyses	10.1002/imt2.175	https://www.bioincloud.tech
gNOMO2	pipeline for integrated multi-omics analyses of microbiomes	10.1093/gigascience/giae038	https://github.com/muzafferarikan/gNOMO2
VeTAPRH (Vertebrates Taxonomic Assignment Protocol)	A Taxonomic Assignment Protocol for Vertebrates Applied to eDNA Metabarcoding Data	10.3897/biss.8.141746
LocalHGT	ultrafast horizontal gene transfer detection method from large microbial communities	10.1093/nar/gkae515	https://github.com/deepomicslab/LocalHGT
GutMetaNet	comprehensive database and analysis platform for human gut microbiome data		https://gutmetanet.deepomics.org/
VMH (Virtual Metabolic Human) database			https://www.vmh.life/
TreeGrafter	phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations	10.48550/arXiv.1802.07304	https://github.com/pantherdb/TreeGrafter
HGTree v2.0	Database of Horizontally Transferred Genes Determined by Tree Reconciliation		http://hgtree2.snu.ac.kr/
DFAST_QC	quality assessment and taxonomic identification tool for prokaryotic Genomes	10.1186/s12859-024-06030-y	https://dfast.ddbj.nig.ac.jp/dqc/submit/
NMDC Data and Metadata R and Python Sample Jupyter Notebooks			https://github.com/microbiomedata/nmdc_notebooks
MicrobiomeNet	comprehensive database that brings together known statistical associations and genome-scale metabolic models (GEMs)	10.1093/nar/gkae944	https://www.microbiomenet.com/
MicroKPNN-MT	predicting human phenotype based on microbiome data	10.1093/bioadv/vbae203	https://github.com/mgtools/MicroKPNN-MT
BlobToolKit	Identification and analysis of non-target data in all Eukaryotic genome projects	10.1534/g3.119.400908	https://blobtoolkit.genomehubs.org/
kMetaShot	fast and reliable taxonomy classifier for metagenome-assembled genomes	10.1093/bib/bbae680	https://github.com/gdefazio/kMetaShot
Prophage-DB	comprehensive database to explore diversity, distribution, and ecology of prophages	10.1186/s40793-024-00659-1	https://github.com/AnantharamanLab/Prophage-DB
Human Microbiome Compendium	dataset of the human microbiome	10.1016/j.cell.2024.12.017	https://microbiomap.org/
LADiM	Lagrangian Advection and Diffusion Model		https://github.com/bjornaa/ladim1
Fundamentals of Biological Data Analysis			https://github.com/kaumudiprabhakara/fundamentals-of-biological-data-analysis/
BalticMicrobeDB	interface to meta-omic data for the Baltic Sea	10.1038/sdata.2018.146	https://barm.scilifelab.se
Baltic Sea Reference Metagenome (BARM)	A set of tools that are useful to reuse the Baltic Sea Reference Metagenome	10.1038/sdata.2018.146	https://github.com/EnvGen/BARM_tools
GAM-NICHE	build Species Distribution Models (SDMs) under the ecological niche theory	10.57762/fzpy-6w51	https://github.com/Fundacion-AZTI/gam-niche
EukDetect	identify eukaryotes in shotgun metagenomic sequencing data	10.1186/s40168-021-01015-y	https://github.com/allind/EukDetect
SimpleMetaPipeline	metabarcoding pipeline	10.1111/2041-210X.14434	https://github.com/J-Cos/SimpleMetaPackage
Bin Chicken	targeted metagenomic coassembly for the efficient recovery of novel genomes	10.1101/2024.11.24.625082	https://aroneys.github.io/binchicken/
Mendelian randomization	distinguish correlation from causation in observational data	10.1038/s41467-019-14156-4	https://www.mendelianrandomization.com/index.php/software-code
Metagenomic Estimation of Dietary Intake (MEDI)	quantifying food-derived DNA in human faecal metagenomes	10.1038/s42255-025-01220-1	https://github.com/Gibbons-Lab/medi
OptimOTU	taxonomically aware approach to OTU clustering	10.48550/arXiv.2502.10350	https://github.com/brendanf/optimotu
FST-based Assessment of Variability across vectors of relative Abundances (FAVA)	Quantifying compositional variability in microbial communities	10.1073/pnas.2413211122	https://maikemorrison.github.io/FAVA/
Global Inventory of Floras and Traits (GIFT)	An R package to access the Global Inventory of Floras and Traits	10.1111/2041-210X.14213	https://biogeomacro.github.io/GIFT/
SpeSpeNet	interactive and user-friendly tool to create and explore microbial correlation networks	10.1093/ismeco/ycaf036	https://tbb.bio.uu.nl/SpeSpeNet/
Happy Belly Bioinformatics	resource for bioinformatics beginners		https://astrobiomike.github.io/
b3gbi	R package for analysing biodiversity data from GBIF data cubes		https://github.com/b-cubed-eu/b3gbi
gcube	R package for biodiversity data simulation		https://github.com/b-cubed-eu/gcube
eDNAjoint	R package for interpreting paired or semi-paired environmental DNA and traditional survey data in a Bayesian framework	10.1111/2041-210X.70000	https://github.com/ropensci/eDNAjoint
ProteoSeeker	Metagenomic Analysis Tool forAccessible and Comprehensive Metagenomic Exploration	10.1002/advs.202414877	https://github.com/SkretasLab/ProteoSeeker
DIVAnd (Data-Interpolating Variational Analysis in n dimensions)	performs an n-dimensional variational analysis/gridding of arbitrarily located observations	10.5194/gmd-7-225-2014	https://github.com/gher-uliege/DIVAnd.jl
COSMO Site	provide information on sea surface currents in the Mediterranean basin and around the Iberian Peninsula	10.1080/1755876X.2022.2102357	https://cosmo.icm.csic.es
Taxoniq	Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data		https://github.com/taxoniq/taxoniq
Ecological Marine Unit (EMU) Explorer	web-based application that is used to explore different water characteristics available from NOAA’s World Ocean Atlas		https://livingatlas.arcgis.com/emu/
NOAA Ocean Exploration Video Portal			https://www.ncei.noaa.gov/access/ocean-exploration/video/
ORDNA (ORDination via Deep Neural Algorithm)	Deep-learning-based ordination for raw environmental DNA samples	10.1111/2041-210X.70033	https://gitlab.renkulab.io/dnai/ordna ; https://gitlab.renkulab.io/dnai/ORDNA-plots
rCRUX	rapid and versatile tool for generating metabarcoding reference libraries in R	10.1002/edn3.489	https://github.com/CalCOFI/rCRUX
refdb	Management of DNA reference libraries	10.1111/1755-0998.13723	https://fkeck.github.io/refdb/
Meta-Fish-Lib	generalised, dynamic DNA reference library for metabarcoding of fishes		https://github.com/genner-lab/meta-fish-lib
Phytool	ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations	10.3897/mbmg.5.74096	https://caninuzzo.shinyapps.io/phytool_v1/ ; https://doi.org/10.57745/TIRNFD
SAND-UP (Strange ASV Names Detector Using Phylogenetic trees)	detect possible misassigned ASVs or refine the taxonomic assignment of some ASVs		https://github.com/Enorya/SAND-UP
eDITH (eDNA Integrating Transport and Hydrology)	explicit interpretation and prediction of environmental DNA (eDNA) data collected from river networks		https://lucarraro.github.io/eDITH/articles/eDITH.html
mGPS (Microbiome Geographic Population Structure)	microbiome fine-scale biogeography tool maps the transfer of antimicrobial resistance genes	10.1093/gbe/evae209	https://github.com/YaliZhang98/mGPS ; https://github.com/YaliZhang98/mGPS_interface
WEST COAST ESTUARIES EXPLORER			https://estuaries.pacificfishhabitat.org
Global Ecosystem Typology			https://global-ecosystems.org
lefser	implementation of LEfSe in R	10.1093/bioinformatics/btae707	https://github.com/waldronlab/lefser
ProtectedSeas Navigator			https://navigatormap.org
ParAquaSeq	Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites	10.1111/1755-0998.14099	https://github.com/ParAqua-COST/ParAquaSeq_Repository
How to Interpret Statistical Models With marginaleffects			https://marginaleffects.com
q2-predict-dysbiosis (Q2PD)	function-based gut microbiome health index	10.1101/2023.12.04.569909	https://github.com/Kizielins/q2-predict-dysbiosis
ReLTER	R interface for Environmental Observation in Long Term Ecological Research	10.1016/j.ecoinf.2024.102915	https://github.com/ropensci/ReLTER/
QCforSeqCode	Snakemake Pipeline to check the requirements for a prokaryotic assembly to be included in the SeqCode initiative		https://github.com/richardstoeckl/QCforSeqCode
EcoFoldDB	Protein structure-guided functional profiling of ecologically relevant microbial traits at the metagenome scale	10.1101/2025.04.02.646905	https://github.com/timghaly/EcoFoldDB
fastreeR	Fast Tree Reconstruction Tools for Genomics	10.1186/s12859-016-1186-3	https://github.com/gkanogiannis/fastreeR
TaxSEA	rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases	10.1093/bib/bbaf173	https://shiny.taxsea.app/
vAMPirus	amplicon processing and analysis program for studying viruses	10.1111/1755-0998.13978	https://github.com/Aveglia/vAMPirus
BOLD v4	Centralized Bioinformatics Platform for DNA-Based Biodiversity Data	10.1007/978-1-0716-3581-0_26	https://v4.boldsystems.org
Haplotype-level metabarcoding of freshwater macroinvertebrate species	prospective tool for population genetic analysis	10.1371/journal.pone.0289056	https://figshare.com/articles/dataset/Metabarcoding-inferred_haplotyping/15090180/1
bugphyzz	data resource and software for enrichment analysis of microbial physiologies		https://github.com/waldronlab/bugphyzz
BEREN	A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data	10.1101/2024.10.09.617401	https://gitlab.com/benminch1/BEREN
samestr	identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles	10.1186/s40168-022-01251-w	https://github.com/danielpodlesny/samestr
unikseq2	Unique (& conserved) region identification in DNA sequences, using k-mers	10.1111/1755-0998.70014	https://github.com/bcgsc/unikseq
Extremophiles Genomic Signature Analysis	uncover new microbial organism pairs whose genomic signatures are similar, despite their maximal taxonomic differences	10.1101/2025.06.04.657665	https://github.com/Kari-Genomics-Lab/Extreme_Env_2
CODARFE (COmpositional Data Analises with Recursive Feature Elimination)	Unlocking the prediction of continuous environmental variables based on microbiome	10.1093/gigascience/giaf055	https://github.com/alerpaschoal/CODARFE
Microbial load predictor (MLP)	R function to predict the fecal microbial load (total microbial cell count per gram or cell density) based on the taxonomic profile of the human gut microbiome	10.1016/j.cell.2024.10.022	https://github.com/grp-bork/microbial_load_predictor
ROCK	digital normalization of whole genome sequencing data	10.21105/joss.03790	https://gitlab.pasteur.fr/vlegrand/ROCK
mbX	An R Package for Streamlined Microbiome Analysis	10.3390/stats8020044	https://github.com/utsavlamichhane/mbX-R-package/
PICRUSt2-SC	an update to the reference database used for functional prediction within PICRUSt2	10.1093/bioinformatics/btaf269	https://github.com/picrust/picrust2
Speciation & Population Genomics: a how-to-guide			https://speciationgenomics.github.io/
MiCoDe (Microbiome Community Detector)	cluster a network of microbial taxa into communities using a Bayesian weighted stochastic block model	10.1093/bioinformatics/btaf384	https://lce.biohpc.swmed.edu/micode/ ; https://github.com/klutz920/MiCoDe
ATCCfinder	identify commercially available American Type Culture Collection strains based on sequence queries	10.7717/peerj.19832	https://github.com/lanl/ATCCfinder
Resources for Learning Bioinformatics and Computational Biology			https://learnbioinformatics.org
A-microbiologist-wants-to-compute	list of learning online resources related to microbiome computational science and tools		https://github.com/SvetlanaUP/A-microbiologist-wants-to-compute
MBPD	A multiple bacterial pathogen detection pipeline for One Health practices		https://github.com/LorMeBioAI/MBPD
taxburst	sunburst charts for taxonomy, based on Krona		https://github.com/taxburst/taxburst
BOLD Library Curation Pipeline	Snakemake pipeline for processing and curating BOLD Systems barcode reference sequence data		https://github.com/bge-barcoding/bold-library-curation
Library Curation Tool	curate records from BOLD database		https://github.com/bge-barcoding/BGE_library_curation_tool
PIMENTO	A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants	10.1101/2025.07.04.663168	https://github.com/EBI-Metagenomics/PIMENTO
eDNA2IQI	automates infaunal quality index (IQI) prediction from raw FASTQ files	10.1016/j.aquaculture.2025.743126	https://github.com/SAMS-UK/eDNA2IQI
eDNAoccupancy	R package for multi-scale occupancy modeling of environmental DNA data	10.1111/1755-0998.12735	https://code.usgs.gov/wetland-and-aquatic-research-center/ednaoccupancy
ECOSYSMIC	Genome-scale community modelling	10.1038/s41467-024-46374-w	https://gitlab.univ-nantes.fr/ecosysmic
APEX pathogen	predicting species-specific antimicrobial activity against pathogens using deep learning	10.1038/s41564-025-02061-0	https://gitlab.com/machine-biology-group-public/apex-pathogen
Database of Antimicrobial Activity and Structure of Peptides (DBAASP)		10.1093/nar/gkaa991	https://dbaasp.org/home
DRAMP (Data repository of antimicrobial peptides)		10.1093/nar/gkae1046	http://dramp.cpu-bioinfor.org
Antimicrobial Peptide Database (APD)		10.1093/nar/gkh025	https://aps.unmc.edu
ggClusterNet 2	R package for microbial co-occurrence networks and associated indicator correlation patterns	10.1002/imt2.70041	https://github.com/taowenmicro/ggClusterNet
microbetag	simplifying microbial network interpretation	10.1186/s13059-025-03769-2	https://github.com/msysbio/microbetag
WhereDoGGo	prokaryotic phylogenomics		https://github.com/MEDEAlab/WhereDoGGo
Omnicrobe	database of microbial habitats and phenotypes	10.1371/journal.pone.0272473	https://forgemia.inrae.fr/omnicrobe
The Microbe Directory (TMD)	a centralized database for biological interpretation of microbiome data	10.1093/database/baaf060	https://themicrobedirectory.shinyapps.io/website/
hvrlocator	identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR)	10.1101/2025.07.24.666487	https://github.com/fbcorrea/hvrlocator
MiCoDa (Microbial Community Database)	searchable database that hosts curated and processed 16S rRNA gene amplicon sequences		https://micoda.idiv.de/v1
OceanOmics-amplicon-nf (inluding FAIRe-fied Hydronaut)	creates a phyloseq object from eDNA amplicon data		https://github.com/MinderooFoundation/OceanOmics-amplicon-nf
Metahood	snakemake pipeline aimed at general analysis on metagenomic shrots reads		https://github.com/Sebastien-Raguideau/Metahood
ASVmaker	generate reference databases for allocating amplicon sequencing data	10.3390/plants12213678	https://github.com/cplessis/ASVmaker
EUKARYOME	community-curated research database for nuclear ribosomal 18S rRNA (SSU), internal transcribed spacer (ITS), and 28S rRNA (LSU) markers for all eukaryotes	10.1093/database/baae043	https://eukaryome.org
biodumpy	A Comprehensive Biological Data Downloader		https://biodumpy.readthedocs.io/en/latest/index.html
PhILR (Phylogenetic Isometric Log-Ratio) Transform		10.7554/eLife.21887	https://bioconductor.org/packages/release/bioc/html/philr.html
StrataSeq	A Workflow for Rapid Development of Molecular Databases for Hard-To-Identify Species	10.1002/ece3.72375	https://figshare.com/articles/dataset/Tables_S1_S2_S3_S4/28622285
AquaX	An enhanced and revised AquaMaps framework to model marine species distributions and biodiversity	10.1101/2025.10.19.683322	https://www.aquamaps.org
SelNeTime	inferring effective population size and selection intensity from genomic time series data	10.1101/2024.11.06.622284	https://forge.inrae.fr/genetic-time-series/selnetime
MMonitor	Real-Time Monitoring of Microbial Communities Using Long Reads	10.1101/2025.09.08.674848	https://www.mmonitor.org
eDNAPlus	A Unifying Modeling Framework for DNA-based Biodiversity Monitoring	10.1080/01621459.2024.2412362	https://datadryad.org/dataset/doi:10.5061/dryad.4f4qrfjjb
Joint species distribution modelling (JSDM) to predict distributions of vulnerable marine ecosystems (VMEs)		10.1007/s10531-024-02904-y	https://github.com/Fabrice-Stephenson/Using_JSDM_to_predict_VME
MetaGraph (Google for DNA)	scalable construction of annotated genome graphs and sequence-to-graph alignment	10.1038/s41586-025-09603-w	https://github.com/ratschlab/metagraph ; https://metagraph.ethz.ch/search
MAMBO	analyze eDNA metabarcoding sequence data from multiple trophic levels to identify drivers and patterns of biodiversity		https://github.com/nvpatin/MAMBO
Compute PTR (CoPTR)	a tool for computing peak-to-trough ratios (PTRs) from complete reference genomes and assemblies	10.1101/gr.275533.121	https://github.com/tyjo/coptr

Tools image: Designed by vectorpouch / Freepik