PyPI Stats

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 404 91
songweizhi
metachip

Horizontal gene transfer (HGT) identification pipeline

4K 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.

4K 37 2
khyox
recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

3K 101 7
Ecogenomics
gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

3K 593 97
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

2K 332 62
trytoolchest
toolchest-client

Python client for Toolchest

2K 15 0
prophyle
prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

2K 36 5
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.

2K 18 0
caozhichongchong
arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes

2K 37 12
anuradhawick
pykmertools

kmertools is a k-mer based feature extraction tool designed to support metagenomics and other bioinformatics analytics.

2K 45 3
gobics
cocopye

Feature-based prediction of genome quality indices

1K 2 0
BigDataBiology
semibin

SemiBin: metagenomics binning with self-supervised deep learning

1K 161 17
genotoul-bioinfo
binette

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

1K 49 2
koszullab
metator

Metagenomic binning based on Hi-C data

1K 28 10
MrOlm
drep

Rapid comparison and dereplication of genomes

1K 338 40
frubino
mgkit

Metagenomics Framework

1K 15 3
zellerlab
gecco-tool

Gene Cluster prediction with Conditional random fields. (renamed to gecco)

1K 84 8
pnnl
hundo

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

1K 13 6
SPAAM-community
amdirt

amdirt: AncientMetagenomeDir Toolkit

988 1 10
jvfe
microview

A reporting tool for aggregating results from taxonomic classification analyses

841 0 0
wwood
singlem

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

819 185 23
taxprofiler
taxpasta

TAXnomic Profile Aggregation and STAndardisation

799 42 8