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 | fast and accurate genomic comparisons | 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 | 10.1101/2021.07.25.453296 | 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/ |
| 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 | |
| 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 | 10.1101/2023.04.18.537298 | 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 |
| AMAW (Automated MAKER2 Annotation Wrapper) | automated gene annotation for non-model unicellular eukaryotic genomes | 10.1101/2021.12.07.471566 | https://bitbucket.org/phylogeno/amaw/src/master/ |
| 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 | Multi-choice 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/ |
| phytools 2.0 | an updated R ecosystem for phylogenetic comparative methods | 10.7717/peerj.16505 | https://github.com/liamrevell/Revell.phytools-v2/ |
| 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 | 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 | 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 | 10.1101/2024.07.11.603040 | 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 |
| 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/ | |
Tools image: Designed by vectorpouch / Freepik