Python

Build bioinformatics pipelines with Snakemake

2015-11-23

Snakemake is a Pythonic variant of GNU Make. Recently, I learned how to use it to build and launch bioinformatics pipelines on an LSF cluster. However, I had trouble understanding the documentation for Snakemake. I like to learn by trying simple examples, so this post will walk you through a very simple pipeline step by step. If you already know how to use Snakemake, then you might be interested to copy my Snakefiles for RNA-seq data analysis here.