Snakemake - A Friendly Introduction

Tue, Jan 26, 2021 1-minute read

I made a tutorial in Snakemake for RSG-Nordic and RSG-Sweden. You can access the full tutorial with data, scripts and solutions at GitHub.

Presentation slides are available here

But, why learn Snakemake? In brief:

Snakemake is a workflow-based system built to make reproducible analyses easy to build, extend and rerun.

There are several arguments for using it in your bioinformatics analyses:

  • Reproducibility - preserve the exact sequence of commands used to generate certain results.
  • Modularity - giving your analysis flexibility, and making it easy to follow the analysis flow.
  • Ease of parallel processing - optimally use your resources with minimal effort.
  • Support for managing versions in containers such as Docker or Singularity.

With that said, I think you will find Snakemake a powerful addition in your set of analysis-tools, well worth the relatively limited time and effort needed to pick up.