InSilicoSeq
a sequencing simulator
Latest release 1.5.3 - Updated - 77 stars
vsearch
Versatile open-source tool for microbiome analysis
Latest release 2.15.2 - Published - 442 stars
pnnl-atlas
ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscri...
Latest release 1.0.32 - Updated - 147 stars
metagenome-atlas
ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscript...
Latest release 2.0.0 - Updated - 147 stars
biomartr
Genomic Data Retrieval
Latest release 0.9.2 - Updated - 115 stars
drep
De-replication of microbial genomes assembled from multiple samples
Latest release 3.2.2 - Updated - 95 stars
MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteri...
Latest release 3.0.13 - Updated - 83 stars
recentrifuge
Robust comparative analysis and contamination removal for metagenomics
Latest release 1.3.3 - Updated - 60 stars
spacegraphcats
tools for biological assembly graph neighborhood analysis
Latest release 2.0 - Updated - 92 stars
ngless-cwl
ngless wrappers for common operations and use with CWL workflows
Latest release 0.0.2 - Updated - 89 stars
enrichm
enrichm is a toolbox for comparing the functional composition of population genomes
Latest release 0.6.4 - Updated - 48 stars
metator
A pipeline for binning metagenomic datasets from metaHiC data.
Latest release 1.1.4 - Updated - 11 stars
cami-amber
AMBER: Assessment of Metagenome BinnERs
Latest release 2.0.2 - Updated - 11 stars
prophyle
ProPhyle metagenomic classifier
Latest release 0.3.3.1 - Updated - 22 stars
hundo
Amplicon processing protocol
Latest release 1.2.8 - Updated - 14 stars
ymp
Flexible multi-omic pipeline system
Latest release 0.2.1 - Updated - 13 stars
arg-ranker
Ranking the risk of antibiotic resistance for genomes/metagenomes
Latest release 2.8.1 - Updated - 5 stars
umgap
The Unipept Metagenomics Analysis Pipeline
Latest release 0.3.7 - Updated - 4 stars
MetaLonDA
Metagenomics Longitudinal Differential Abundance Method
Latest release 1.1.8 - Updated - 2 stars
kraken-biom
Create BIOM-format tables from Kraken output.
Latest release 1.0.1 - Published - 29 stars
singlem
Find de-novo operational taxonomic units (OTUs) from metagenome data
Latest release 0.13.2 - Updated - 21 stars
panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *i...
Latest release 1.3 - Updated - 19 stars
grabseqs
Easily download reads from next-gen sequencing repositories like NCBI SRA
Latest release 0.7.0 - Updated - 15 stars
MicrobeCensus
A command-line tool for estimating average genome size from shotgun sequence data
Latest release 1.2.1 - Updated - 14 stars
superfocus
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
Latest release 0.35 - Updated - 10 stars
meta-sparse
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to pr...
Latest release 0.1.12 - Updated - 8 stars
S3N2Bin
Metagenomic binning with semi-supervised siamese neural network
Latest release 0.1.1 - Updated - 7 stars
magpurify
Identify and remove incorrectly binned contigs from metagenome-assembled genomes.
Latest release 2.1.2 - Updated - 7 stars
tiara
A tool for classifying metagenomic data
Latest release 1.0.2 - Updated - 7 stars
MGLEX
MGLEX - MetaGenome Likelihood EXtractor
Latest release 0.2.1 - Updated - 6 stars
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