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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 former 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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Now that you have completed the above tutorials you have accomplished the necessary skills for basic genome sequence analysis and identify real genetic variants out of the noise of genomic sequencing. The next step will be in learning additional skills to refine your abilities to better suit your personal analysis. The remaining tutorials should be completed based on what you think would be the most helpful to your specific analysis, we've divided them up into broad categories, and tried to explain what the purpose of each tutorial is, but if you are unsure just ask.
Bacterial Centric Tutorials
Tutorial: Breseq basics
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
Method based Tutorials that may be of help regardless of sample type
Tutorial: Genome Assembly Using Velvet
Tutorial: Exome Capture Metrics
Tutorial: Error Correction (Molecular Indexing)
Thursday May 26th. Day 4 – 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. While we have added some new tutorials to the above sections, we also introduced some tutorials here that are more methodology based and less sample based. Choose your own tutorial, and please don't hesitate to ask us what tutorials would be good for you to be working on given your data!
The second half of today's class will be going over how to do things the normal way on TACC which means using the job submission system and commands files.
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Presentation:
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