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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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Presentation: Errors: Where do they come from and how do we identify them as noise rather than signal?
Bonus Presentation: Alternative Library Prep Methods - for when errors really do matter.
Tutorial: Visualization: Integrated Genome Viewer Tutorial
Tutorial: Visualization: Bacterial genome variants the easiest way – breseq
At this point in the course, you have the basic tools that will help you regardless of what type of research you are involved in. The remainder of the course is full of topics that are more specific to different research areas. They are divided into broad categories to help you decide which ones you want to complete during the remaining time. If you are unsure just ask and I'll help identify ones which may be more applicable to your work.
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Tutorial: Human Trios Analysis
Tutorial: Comparing Multiple samples
Tutorial: GATK
Tutorial: Exome Capture Metrics – with GATK
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Tutorial: Error Correction (Molecular Indexing)
Tutorial: Annotating plasmids with pLannotate
Friday, June 24th. Day 5 – User specific tutorials (continued) and TACC the "normal" way
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