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This class has been taught multiple times in the last few years. We wish to acknowledge a great deal of help with creating these web pages and materials from previous instructors of the Intro to NGS Bioinformatics course taught in May 2013 and the Genome Variant Analysis Course 2014 taught in May 2014. Two individuals warrant special mention, the director of the GSAF Scott Hunicke-Smith, and Jeffrey Barrick have been the driving force behind this class for a number of years, and the majority of the tutorials presented here were developed by them or adapted from their work. |
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Friday May 29th. Day 4 – "(Rare) Variant Detection in Populations"
Presentation: How to know if a variant matters?
Tutorial: Annotating variants with annovar
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- YouTube video explaining illumina sequencing
- NGS Course Resources Tool List
- GSAF adaptor and barcode sequence resource
- Working on TACC from your Mac or PC
- Scott's list of linux one-liners
- Installing Virtual machine & Linux on Windows
- Example BWA alignment script
- Variant calling with GATK (SPHS)
- Visualize mapped data at UCSC genome browser (AB)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- SRA toolkit and Exercises (AB)
- Shell Scripting (SPHS/AB)
- Installing Linux tools (JB)
- Custom Genome Databases
- Evaluating & Visualizing assemblies (bacterial, SPHS)
- Genome Assembly Examples (SPHS)
- Tutorial: Genome Assembly (velvet) (SPHS)
- Visualize mapped data at UCSC genome browser (AB)
- ddRAD (Stacks tutorial: http://evomics.org/wp-content/uploads/2013/03/cesky_2014_RAD_tutorial_updated.pdf) , Tn-Seq?