Microbiome Python Packages

scikit-bio

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

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

microbiomekg

A microbiome knowledge graph on kglite, with the evidence model as the point.

micom

Python package to study microbial communities using metabolic modeling.

dram-bio

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

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

miscoto

Python package for large-scale community selection in microbiota

amon-bio

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

singlem

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

redbiom

Sample search by metadata and features

micone

The Microbial Co-occurrence Network Explorer

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

microberx

MicrobeRX

biomcp-server

🧬 BioMCP — bioinformatics MCP server: 83 tools · 43 databases · PubMed/NCBI/BLAST/PDB/UniProt/enrichment · `pip install biomcp-server` · 生信 MCP 服务器

amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

dbbact-calour

dbBact (https://dbbact.org) interface for Calour (https://github.com/biocore/calour) for microbiome 16S analysis

compositional

Python package for compositional data analysis including CLR/ILR, proportionality, partial correlation with basis shrinkage, and visualizations.

qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

deeptaxa-rrna

Hybrid CNN-BERT deep learning for hierarchical taxonomic classification of 16S rRNA sequences

microbiome-toolbox

Early Life Microbiome Toolbox

woltka

Woltka: a versatile meta'omic data classifier

mibiscreen

Prediction tool for Microbiome based Remediation

intelligrate

Diversity-aware sample selection and kNN-based extrapolation of a partially measured data layer to the complete dataset.

famli

Functional Analysis of Metagenomes by Likelihood Inference