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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: Structural Variant Calling
Tutorial: Using samtools to identify SNVs
Tutorial: Using SVDetect to identify SV
Bonus Presentation: Read Mapping Details and File Formats
Wednesday, June 22nd. Day 3 – Visualization and User specific tutorials
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.
Bacterial Centric Tutorials
Tutorial: Advanced Breseq
Tutorial: breseq with multiple references
Tutorial: Evaluating Error Correction Using Breseq
Human and Higher Eukaryote Centric Tutorials
Tutorial: Human Trios Analysis
Tutorial: Comparing Multiple samples
Tutorial: GATK
Tutorial: Exome Capture Metrics – with GATK
Tutorial: Annotating with Annovar
Method based Tutorials that may be of help regardless of sample type
Tutorial: MultiQC - fastQC summary tool for multiple samples
Tutorial: Read processing with fastp
Tutorial: Genome Assembly
Tutorial: Novel DNA identification
Tutorial: Advanced mapping
Tutorial: Error Correction (Molecular Indexing)
Tutorial: Annotating plasmids with pLannotate
Friday, June 24th. 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 any remaining time to go through tutorials and ask any remaining questions.