Bash for Bioinformatics
  • Type Learning
  • Level Intermediate
  • Time Weeks
  • Cost Free
Additional Details

Bash for Bioinformatics

Issued by Fred Hutchinson Cancer Center Data Science Lab

In this course, you will apply Bash scripting to run bioinformatics software and R and Python scripts on the Fred Hutch high performance cluster. You will also learn how to scale up your work using batch jobs and workflow languages in a reproducible way.

  • Type Learning
  • Level Intermediate
  • Time Weeks
  • Cost Free
Additional Details

Skills

Earning Criteria

  • Apply bash scripting to execute alignment, and Python/R scripts.
  • Navigate and process data on the different filesystems available at FH
  • Manage software dependencies reproducibly using container-based technologies such as Docker/Apptainer containers or EasyBuild modules.
  • Articulate basic HPC architecture concepts and why they’re useful in your work
  • Leverage bash scripting to execute batch jobs on a high performance cluster.
  • Utilize workflow managers such as miniWDL/PROOF to process multiple files in a multi-step WDL workflow.