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This workshop is intended for researchers in genomics and related fields with little to no experience with the command-line, large-scale computing, or with computational genomics tools and workflows. The topics covered will include: an introduction to the Linux command-line, and introduction to large-scale computing and submitting jobs to a typical high-performance computing resource, running a typical raw data to variant calling workflow for Illumina data, and strategies for running the same workflow on multiple files in parallel, to take advantage of the cluster architecture.

Many parts of this lesson (including the website design) borrow from the lesson materials of Software Carpentry an organization dedicated to teaching researchers and scientists the basic "lab skills" for computing. You may be interested in Software Carpentry's other lessons on topics like programming in R/Python, version control with Git/GitHub, etc.,

Prerequisites

Some knowledge of the Unix shell is desired, but not strictly necessary. Some knowledge of genetics is required; e.g., you should know what the terms "genome" and "mutation" refer to. {: .prereq}

Checklist

1. Obtain an account on the Palmetto Cluster, if you don't have one already. Instructions for requesting an account are available here.

2. Familiarize yourself with the procedure for logging-in to the cluster by following the instructions here.

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