Bash for Bioinformatics

Who this course is for:

  • Have you needed to align a folder of FASTA files and not know how to do it?
  • Do you want to automate an R or Python script you wrote to work on a bunch of files?
  • Do you want to do all of this on a high performance cluster (HPC)?

If so, this course is for you! We will learn enough bash scripting to do useful things on the Fred Hutch cluster and automate the boring parts.

Registration is not open yet! Explore the course materials

Class information

  • Quarters Offered: Fall 2025, Spring 2026

  • Dates: Spring 2026: May 15, 22, 29, June 5

  • Time: Fridays Noon - 1:30pm PT

  • Time commitment: 4 weeks of 1.5 hour classes and 1-2 hours of practice outside class.

  • Audience: FH Research Staff wanting to execute jobs and process genomic data on the gizmo cluster.

  • Prerequisites: Intro to FH Cluster Computing

  • Followed by: None

Learning Objectives (LOs)

  • Articulate basic HPC architecture concepts and why they’re useful in your work

  • Apply bash scripting to execute alignment, and Python/R scripts

  • Navigate and process data on the different filesystems available at FH

  • Leverage bash scripting to execute jobs on a high performance cluster

  • Execute batch processing of multiple files in a project

  • Manage software dependencies reproducibly using container-based technologies such as Docker/Apptainer containers or EasyBuild modules

Frequently Asked Questions

  • How often is this class taught?

    This class is offered twice a year (currently fall and spring quarters). Check the schedule to see when it will next be offered.

  • Can I work through the materials without taking the class?

    Yes, you can access the course materials on your own any time.

  • Can I get a badge without taking the class?

    You need to complete the live class to get a badge.

  • What kind of computing resource do I need?

    You will need to have access to the command line, a network connection to Fred Hutch's research network, and have your Fred Hutch account approved by Scientific Computing. See instructions on the registration form.

  • Can I take the class if I’m not an employee at Fred Hutch?

    The class is open to members of the Cancer Consortium including Fred Hutch, the University of Washington, and Seattle Children’s Hospital. But note that the content is focused on accessing the Fred Hutch cluster. Some instructions may not apply to clusters at other institutions.

  • Can I take more than one class at once?

    You can, but we recommend you don’t mix R and Python at the same time, because it can be confusing to switch between the two.

  • Can I take this class more than once?

    You can sign up more than once, but be aware that there is tyspically a waitlist. We will prioritize students who have not taken the class. If there is room you are welcome to take it again.