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
- 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
Day 4: Post-Alignment Analysis
- SAM format and samtools
- Analysis using BEDTools
- Odds and ends