Search 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

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

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.

gtdbtk

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

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

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

toolchest-client

Python client for Toolchest

arg-ranker

Ranking the risk of antibiotic resistance for genomes/metagenomes

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.

pykmertools

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

binette

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

mgkit

Metagenomics Framework

semibin

SemiBin: metagenomics binning with self-supervised deep learning

drep

Rapid comparison and dereplication of genomes

gecco-tool

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

metator

Metagenomic binning based on Hi-C data

hundo

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

cocopye

Feature-based prediction of genome quality indices

amdirt

amdirt: AncientMetagenomeDir Toolkit

singlem

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

microview

A reporting tool for aggregating results from taxonomic classification analyses

taxpasta

TAXnomic Profile Aggregation and STAndardisation