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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 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 Analysis

Core NGS Tools -- Resources


 Info for the instructors

meet 8 am Monday – students will start ariving ~8:30.

room key – should be automatically opened at 7:30 am

name tags – Rayna will provide; pick up from her Friday at Big Data

sign in sheet & sign to room – Amelia

visit room to check out video hookups, lab computers – Friday 12:45 - 1pm

  • last year all the classroom computers used credentials userid: student password: hookem
  • check whether this is still true or if UT EIDs are required

print cheat sheets – Amelia

obtain stampede allocation info from Hans – Anna

add attendees credentials to stampede login8 – Anna

course artifacts – /corral-repl/utexas/BioITeam/core_ngs_tools – make subdirctories & chmod 777 everything

web URL:, corresponds to /corral-repl/utexas/BioITeam/web



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