metaphlan

Analyzing shotgun data

Import and process results from a metagenomics output e.g. metaphlan2

Benchmarking various taxonomic classifiers for profiling soil metagenomic data, with scripts and tools tailored for fungal, bacterial, and archaeal genome identification.

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

A simple R package to convert MetaPhlAn 4 output profiles to a phyloseq object.

A metagenomics pipeline project that runs sequencing QC, taxonomic profiling, assembly, gene prediction, and functional annotation using common CLI tools (FastQC, MetaPhlAn, MEGAHIT, GeneMarkS, BLAST) plus light Python/shell automation.

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

Jacobs Lab UCLA : Preprocess shotgun metagenomics data on the UCLA supercomputer, using either Biobakery tools or Kraken/Bracken.

An analysis of the metagenomic profiles of various colorectal cancer patients and healthy controls to try and identify distinct signatures between various stages of the disease.

Metagenomics of cured meat products on an ordinary Windows PC with 16 GB of RAM: from sequencing reads to taxa with MetaPhlAn 4. Double-click installation, no terminal.