Metagenomics Python Packages

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

insilicoseq

:rocket: A sequencing simulator

metachip

Horizontal gene transfer (HGT) identification pipeline

drep

Rapid comparison and dereplication of genomes

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

metaphlan

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

dram-bio

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

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.

semibin

SemiBin: metagenomics binning with self-supervised deep learning

gtdbtk

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

pykmertools

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

mgnifam

Build protein families from sequence clusters by iterative HMM search over very large databases — streaming, deterministic, pyHMMER-based.

binette

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

viralquest

A user-friendly pipeline for viral diversity analysis and characterization.

krakenparser

🗂️Parse multiple Kraken2 reports into CSV files on 6 taxonomical levels

amdirt

AncientMetagenomeDir Toolkit

toolchest-client

Toolchest Python client

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

aviary-genome

A hybrid assembly and MAG recovery pipeline (and more!)

mobiorigin

MobiOrigin classifies bacterial contigs as plasmid, chromosome, phage, or unclassified using sequence, coding and mobility-marker evidence.

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.

metator

Metagenomic binning based on Hi-C data

singlem

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

arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes