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We will meet in Room 7.306 of Robert Lee Moore Hall (RLM).  We encourage you to use the computers provided in the classroom for these tutorial, but you may also bring your personal laptops.

Etherpad

You can jot questions or command lines to share with the class here: https://etherpad.mozilla.org/V1EIko9FS5


Your Instructors

Name

Initials

Affiliation

Expertise

Scott Hunicke-Smith

SPHS

Director GSAF

Everything, if loosely defined (but especially awk)

Jeff Barrick

JB

Molecular Biosciences

Microbes, Perl, C++, Mac, breseq, Miscellanea

Dan Deatherage

DD

Barrick Lab

Unix, Python, NGS Library Prep, Capture, Rare variants

We acknowledge a great deal of help with creating these web pages and materials from other instructors of the Intro to NGS Bioinformatics course most recently taught in May 2013.

Day 1. Linux/TACC Introduction and Read Mapping

Part 1. Linux/TACC Introduction (SPHS)

Part 2. Mapping Reads (JB)

Day 2. Microbial Genome Variation

Part 1. Single-nucleotide variants (JB)

Part 2. Structural variants (JB)

Day 3: Human Genome Variation

Part 1. Overview and the mechanics of calling variants

Part 2. Annotating, filtering, and screening variants; evaluating performance

Day 4: Rare Variant Detection in Populations

Part 1. Sequencing of mixed populations

Part 2. Targeted Sequencing of Molecular Indexed Libraries. 

Resources

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