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.

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.

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

shotgun metagenomics pipeline to obtain relative abundances and pathway abundances

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.