humann

Gut-metagenome multi-kingdom analysis platform: 183-script + Snakemake pipeline, agent-driven mining loop, MCP visualization — VibeCoding-ready

A lightweight, robust, and out-of-the-box metagenomics pipeline based on bioBakery.

Intro guide to using DTU HPC, with LSF job scripts for metagenomics workflows using KneadData, MetaPhlAn, and HUMAnN.

shotgun metagenomics pipeline to obtain relative abundances and pathway abundances

End-to-end clinical shotgun metagenomic pipeline investigating microbial triggers (NOD2/TLR4) of metabolic inflammation, disproving barrier failure and supporting the Host Autonomy model in Type 2 Diabetes.

This repo maintains the definition files used for building singularity images remotely. Each branch maintains a different environment.