Data Carpentry Genomics

This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. The training assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. By the end of the workshop, learners will be able to:

1. structure their metadata, organize and document their genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database,
2. navigate their file systems, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards,
3. use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation,
4. work with Amazon AWS cloud computing and transfer data between their local computer and cloud resources. 

Learners will need to bring a laptop (not a tablet) with any spreadsheet program installed (e.g. LibreOffice, Microsoft Excel). Learners using a Windows machine will also need to download and install PuTTY https://putty.org/ .