How to organize a bioinformatics project: using bash to set up a project directory (CC013)
Channel: Riffomonas Project
Date: 02/07/2020

In this screencast tutorial, Pat Schloss shows how you can organize your projects to increase their reproducibility. To motivate the discussion, Pat lays out a question that we will return to over future episodes: To what degree do inter- and intra-genomic variation limit the interpretation of amplicon sequence variants (ASVs; aka exact sequence variants or ESVs)? Today we'll discuss how to use the command line to create the structure of our project directory and review the value of using relative paths over absolute paths.

Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make. He then turns viewers loose to work through several activities to answer related questions.

The site that contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-07-02-project-organization.



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