This is the home of the Core NGS Tools course, May 2014

This workshop provides an introduction to common analysis tools and file formats currently used in NGS, with emphasis on read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.

We will meet in Room 101B of the Flawn Academic Center (FAC) building.  We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops.

Day 1: Linux/TACC Introduction

Day 2: Raw Sequencing data manipulation

Day 3: Alignment and BAM file manipulation

Day 4: Post-Alignment Analysis

Part 1: Bedtools

Part 1: Odds and ends

Enrichment modules


Link to Etherpad:

Use this to post any questions you have about the lessons and tutorials.

Your Instructors


room key – should be automatically opened at 7:30 am

name tags – Rayna will provide

sign in sheet & sign to room – Amelia

visit room to check out video hookups, lab computers – Rayna will give us time

print cheat sheets – Amelia

obtain allocation info from Hans – Amelia

ask Scott to add attendees credentials to login8 – Anna

meet 8am Monday


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