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
- Getting started at TACC – logging in
- lecture: NGS overview & technology (2017_05-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: Working with raw sequences
- lecture: the FASTQ format (2017_05-NGSintro.pdf, part 2)
- Working with FASTQ files
- lecture: Sequence QC & preparation (2017_05-NGSintro.pdf, part 3)
- QC & pre-processing
- Running batch jobs at TACC (time permitting)
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis