Getting started with Snakemake

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About this course

Targeted audience:

  • bioinformaticians
  • biologists that have experience in running scripts or programmes through command lines
  • An introduction to Snakemake and on why to use workflow tools
  • Example exercises to get familiar with Snakemake


Why should I follow this training session?

If you have routine bioinformatics analyses requiring a series of different tools, this training course is made for you!

Perhaps you’ve already heard of Nextflow and/or Snakemake? These are popular bioinformatics workflow managers designed to minimise the number of manual steps in your analyses. They help you automate, monitor and scale up your analysis pipelines (to the I2BC computing cluster, for example).
In this course, we will introduce you to Snakemake and help you take your first steps using small, simple examples. Of course, feel free to bring along your own analysis pipelines if you wish.

Course organisers:

Emilie Drouineau (GENOMES/REMOD),

Chloé Quignot (PF/BIOI2 – ORCID: 0000-0001-8504-232X),

Claire Toffano-Nioche (GENOMES/SSFA – ORCID: 0000-0003-4134-6844)

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