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This is the home of the Core NGS Tools course, May 2015June 2022, at 

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.



For online attendees, the Zoom URL is:

There will be a short break each day around 10:30am.

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.


Your TACC account will remain on our class  TACC project allocation through June 30, 2022

We will provide access to recordings of each day's materials after the course is over.

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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