Description:

The first step in almost all bioinformatic pipelines is sequence alignment. There are many software tools available to accomplish this task. Choosing an appropriate tool and then using it at scale can be intimidating. This workshop will remove some of the mystery by suggesting aligners for specific tasks and covering the basics of using each suggested tool including: bwa, bowtie2, and minimap2. Participants will compose and run submission scripts for each of these, and we will look at the output they create.

Prerequisite: This workshop requires a laptop with a terminal application installed and expects familiarity with working from the command line or attendance at the Command Line Introduction workshop.

About the series: This workshop series is designed to cover foundational topics in computational genomics for the research community that uses the Genomics Compute Cluster (GCC) at Northwestern. Most workshops can be attended ad hoc, but some of the content builds on itself from week to week, and most require attendance at the first workshop of the series, Command Line Introduction, so please read the description of each. These workshops will be held in person on the Chicago campus. To participate fully, you will need to bring a laptop with you to each workshop.