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I think it important 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 2013 and the Genome Variant Analysis Course taught in 2014-2016. Two individuals warrant special mention, the former director of the GSAF Scott Hunicke-Smith, and Jeffrey Barrick were the driving force behind this class for a number of years, and many of the tutorials presented here were originally developed by them or adapted from their work. |
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Tutorial: Advanced Breseq
Tutorial: Evaluating Error Correction Using Breseq
Human and Higher Eukaryote Centric Tutorials
Tutorial: Human Trios Analysis
Tutorial: Annovar Analysis
Tutorial: Comparing Multiple samples
Tutorial: GATK
Method based Tutorials that may be of help regardless of sample type
Tutorial: MultiQC - fastQC summary tool for multiple samples
Tutorial: Read processing with trimmomatic
Tutorial: Genome Assembly
Tutorial:
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Novel DNA identification
Tutorial: Exome Capture Metrics
Tutorial: Error Correction (Molecular Indexing)
Tutorial: Moving beyond mapping
Friday, June 26th. Day 5 – User specific tutorials (continued) and TACC the normal way
The first half of today's class will be done as a continuation of tutorials that you are most interested in. As was the case yesterday, choose your own tutorial, and please don't hesitate to ask what tutorials would be good for you to be working on given your data! After the break, we will be go over a brief review to put things back in prospective and give you a tutorial on how to do things the 'normal way' on TACC which means using the job submission system and commands files before giving you the rest of the time to go through tutorials and ask any remaining questions.
Presentation: Genome Variant Analysis Review
Tutorial: Job Submissions and end of class summary of actions
Tutorial: Advanced mapping
Tutorial: breseq with multiple references
Post class changes:
Tutorial: Annovar Analysis
Updated to fix for inability to access reference files stored in BioITeam repositories while on idev nodes.
Addressing launcher_creator.py issues
Information for dealing with difficulties with .slurm files generated with the launcher_creator.py script