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This is the home of the Core NGS Tools course, May 2015

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 4.128 of Mezes Hall.  We encourage you to use the computers provided in the classroom, but you may also use your personal laptops.

Day 1: Linux and TACC

Day 3: Alignment and BAM file manipulation

Day 4: Post-Alignment Analys

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



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