Metagenomics Python Packages

metaphlan

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

metachip

Horizontal gene transfer (HGT) identification pipeline

pykmertools

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

insilicoseq

:rocket: A sequencing simulator

krakenparser

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

dram-bio

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

gtdbtk

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

jaeger-bio

Jaeger is a quick and precise tool for detecting phages in sequence assemblies.

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.

drep

Rapid comparison and dereplication of 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.

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes

binette

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

semibin

SemiBin: metagenomics binning with self-supervised deep learning

toolchest-client

Python client for Toolchest

metator

Metagenomic binning based on Hi-C data

amdirt

AncientMetagenomeDir Toolkit

singlem

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

hundo

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

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

pynteny

Query sequence database by HMMs arranged in predefined synteny structure

crocodeel

CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data

gecco

GEne Cluster prediction with COnditional random fields.