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.

shotgun metagenomics pipeline to obtain relative abundances and pathway abundances

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

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

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.

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.