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This is the home of the Core NGS Tools course, May 2017, at https://wikis.utexas.edu/display/CoreNGSTools

This workshop provides an introduction to common analysis tools and file formats currently used in NGS, with emphasis on quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), 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 4.144 of Mezes Hall.  We encourage you to use the computers provided in the classroom, but you may also use your personal laptops.

Day 1: Intro to NGS, Linux and TACC

Day 4: Post-Alignment Analysis

  • Samtools - viewing, counting and sorting your alignment data
  • BedTools - analyzing your aligned data

Resources

 

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