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

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.

insilicoseq

:rocket: A sequencing simulator

dram-bio

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

singlem

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

toolchest-client

Toolchest Python client

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

gtdbtk

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

cocopye

Feature-based prediction of genome quality indices

binette

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

arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes

semibin

Metagenomic binning with siamese neural networks

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.

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

metator

A pipeline for binning metagenomic datasets from metaHiC data.

amdirt

amdirt: AncientMetagenomeDir Toolkit

microview

Generate reports from metagenomics data

drep

Rapid comparison and dereplication of genomes

crocodeel

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

mgkit

Metagenomics Framework

pykmertools

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

hundo

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

superpang

Non-redundant pangenome assemblies from multiple genomes or bins