This repository describes the code and analyses accompanying the MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data manuscript.

The MetaMap bioinformatic pipeline screens human RNA-seq data for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. Simon et al. applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from >17,000 samples from >400 studies relevant to human disease using state-of-the-art high performance computing systems from the Leibniz Supercomputing Centre in Garching, Germany.

1. Detailed information about the MetaMap pipeline and how to execute it on your own data can be found at protocols.io.

2. An R based tutorial describing the statistical analysis of the resulting output can be found in Tutorial_statistical_analysis.html/Rmd files.

3. To facilitate interactive exploration of the MetaMap resource we have developed a webtool. By clicking on the following link you can access the webtool and agree with our data protection policy (as outlined here): MetaMap webtool. The code used to create the webtool can be found here.