edX

Course materials for the edX Data Analysis for Genomics whole genome sequencing module. Course materials include:

• Introduction to sequencing
• Introduction to re-sequencing studies
• The command line & using VirtualBox
• Resequencing workflow
• Quality control
• Read trimming and filtering
• Alignment and marking duplicates
• Calling variants with FreeBayes
• VCF filtering and annotation
• Exploring VCFs with GEMINI

Authors

• Oliver Hofmann (overall course design)
• Shannan Ho Sui
• Meeta Mistry
• Radhika Khetani
• Brad Chapman (building the VM)
• Erik Garrison (all things FreeBayes and variant calling)
• Aaron Quinlan (Gemini tutorial)
• Jessica Chong (Gemini case studies)

Attributions

This course borrows heavily from the FreeBayes tutorial developed by Erik Garrison and course materials from UC Davis, and other online courses such as the Software Carpentry materials.

License

Course materials are made available under an MIT license.