Building a bioinformatics pipeline with SnakeMake

Instructor: Brian McConeghy (UBC)

This course is an introduction to using the Snakemake workflow management system to create reproducible and scalable bioinformatics pipelines. Workflows are written in Python and can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. In this course, we will be writing a Snakemake pipeline that takes DNA reads as input and runs basic QC on them, maps them to a genome of interest, sorts them, indexes them, and calls genomic variants.

Target audience: bioinformatics

Duration: 3 hours

Level: intermediate

Prerequisites: Familiarity with Python, Bash, Bioinformatics tools.

Laptop software: All attendees will need to bring their laptops with wireless access and with a remote SSH client installed (on Windows laptops we recommend the free edition of MobaXterm; on Mac and Linux laptops no need to install anything).