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 and Raw Sequence structure

Part 1: Linux introduction

Day 2: Raw Sequencing Quality Evaluation

Part 1: FASTQ manipulation tools

Part 2: FASTQ manipulation at TACC

Day 3: Alignment and BAM file manipulation

Part 1: Alignment and aligners

Part 2: SAM/BAM format and manipulation

Day 4: Post-Alignment Visualization and Analysis

Part 1: Visualization tools and formats

Part 2: SAM/BAM format and manipulation

Enrichment modules


Link to Etherpad:

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

Your Instructors


Instructors: meet 8am Monday

Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...

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