/snakepipes

Snakemake workflows and wrappers for NGS data processing

Primary LanguagePython

MPI-IE Snakemake workflows : snakePipes

Documentation Status Build Status Citation

snakePipes are our in-house, flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

Workflows available

  • DNA-mapping (normal and allele-specific)
  • ChIP-seq (normal and allele-specific)
  • RNA-seq (normal and allele-specific)
  • scRNA-seq
  • Hi-C

Installation

Currently the workflows don't require installation of the scripts. Simply clone this github repository and modify the configuration files under shared/organisms and shared/paths.yaml with your own paths.

Documentation

For documentation on setup and usage, please visit our read the docs page.