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Metagenomics Python Packages

Python packages with the GitHub topic metagenomics. Sorted by relevance, with stars and monthly downloads.
biobakery
metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

5K 406 91
songweizhi
metachip

Horizontal gene transfer (HGT) identification pipeline

5K 71 18
metagenopolis
meteor

Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.

3K 39 2
HadrienG
insilicoseq

:rocket: A sequencing simulator

3K 224 36
shafferm
dram-bio

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

3K 332 62
wwood
singlem

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

2K 188 23
trytoolchest
toolchest-client

Toolchest Python client

2K 15 0
khyox
recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

2K 102 7
Ecogenomics
gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

2K 598 98
gobics
cocopye

Feature-based prediction of genome quality indices

1K 2 0
genotoul-bioinfo
binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

1K 50 2
caozhichongchong
arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes

1K 37 12
BigDataBiology
semibin

Metagenomic binning with siamese neural networks

1K 161 17
danielzmbp
remag

Recovery of eukaryotic genomes using contrastive learning. A specialized metagenomic binning tool designed for recovering high-quality eukaryotic genomes from mixed prokaryotic-eukaryotic samples.

1K 18 0
prophyle
prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

1K 36 5
koszullab
metator

A pipeline for binning metagenomic datasets from metaHiC data.

1K 28 10
SPAAM-community
amdirt

amdirt: AncientMetagenomeDir Toolkit

1K 1 10
jvfe
microview

Generate reports from metagenomics data

992 0 0
MrOlm
drep

Rapid comparison and dereplication of genomes

972 340 41
metagenopolis
crocodeel

CroCoDeEL is a tool that detects cross-sample (aka well-to-well) contamination in shotgun metagenomic data

957 28 0
frubino
mgkit

Metagenomics Framework

939 15 3
anuradhawick
pykmertools

kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more

845 45 3
pnnl
hundo

:100: Snakemake-based amplicon processing protocol for 16S and ITS sequences.

824 13 6
fpusan
superpang

Non-redundant pangenome assemblies from multiple genomes or bins

795 15 1
    • Data from PyPI, GitHub, ClickHouse, and BigQuery