This repository contains an ATAC-Seq pipeline using Snakemake.

Folders and files should be self-explanatory, however, a few notes:
  1) The doc folder contains various documentation. The "old" subfolder can be safely ignored. See the various PDF files for a (beta) version of the documentation and some other helpful information regarding how to run the pipeline, how to procvess ATAC-Seq data etc.
  2) The example folder is important. Use this to test if you run the pipeline using a small example analysis consisting of two samples.
  3) The src folder contains the source of the project.