UMGAP Case Studies

This page explores several uses of the Unipept MetaGenomics Analysis Pipeline.

Introduction

The Unipept Metagenomics Analysis Pipeline (UMGAP) is a tool for mapping (short) metagenomics reads to taxa, rivalling state of the art alternatives such as Kraken (2014) with the additional benefit of species level identification. UMGAP achieves this by transforming the mapping task into a metaproteomics problem by using various alternative gene predictors on the metagenomics reads and processing the resulting data with the existing Unipept Metaproteomics Analysis Pipeline. Each step in UMGAP is highly configurable.

These case studies assume you have already followed the installation instructions.

Preconfigured analysis of a metagenomics dataset

The easiest way to use UMGAP for a taxonomic analysis of a metagenomic dataset is with one of the 6 preconfigured pipelines. This case study walks you through the complete analysis of 2 short FASTQ files.

Complete configuration walkthrough

This case study shows how to use UMGAP for the taxonomic analysis of a metagenomics dataset. It shows every step of the pipeline in detail, refering to the documentation for alternative options.

Comparative analysis walkthrough

This case study shows how to use UMGAP for the comparative taxonomic analysis of multiple metagenomics datasets. Using a preconfigured pipeline and the visualize script, we show how to create a comparative graphic.