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Note

title	A nod to the past

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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In order to ensure as smooth an experience as possible, the week prior to the course, each participant needs to log into TACC and provide their TACC ID to Dan. Depending on your operating system you should complete either the window or mac tutorial below as well as the TACC tutorial. If you are having difficulties log into the zoom between 12 and 1 any day Tuesday-Friday or send an email if you need to schedule a separate time.

Windows10

MacOS

TACC

Course Schedule

Monday, June 22^nd. Day 1 – "The Basics"

Presentation: General Course Introduction

Tutorial: Introduction to linux and lonestar5

Presentation: Experimental Design

Tutorial: Evaluating raw sequencing data

Tuesday, June 23^rd. Day 2 – "Principles of Variant calling"

Presentation: Read Mapping

Tutorial: Using Bowtie2 to map reads

Presentation: Single Nucleotide Variant Calling

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 24^th. 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: Installing Breseq

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: Novel DNA identification

Tutorial: Exome Capture Metrics

Tutorial: Error Correction (Molecular Indexing)

Tutorial: Moving beyond mapping

Friday, June 26^th. 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.