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.

Day 1: Linux and TACC

• Introduction
• Overview NGS data processing 
• Getting started at TACC

Day 2: NGS workflow overview and raw sequence pre-processing

• Running batch jobs at TACC
• Finish – Overview NGS data processing 
• Start – Pre-processing FASTQ sequences

Day 3: Alignment and BAM file manipulation

• Finish – Pre-processing FASTQ sequences
• Alignment

Day 4: Post-Alignment Analysis

• Samtools - viewing, counting and sorting your alignment data
• Analyzing your aligned experiment with BedTools
• Odds and ends

Resources

• Linux fundamentals

• Core NGS Tools -- Resource lists

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