This is the home of the Core NGS Tools course, May 2016June 2021, 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 4.128 of Mezes Hall. We encourage you to use the computers provided in the classroom, but you may also use your personal laptops.
This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91965141761
There will be a short break each day around 10:30am.
Your TACC account will remain on our class' TACC project allocation through June 30, 2021.
Contact us for access to recordings of each day's materials after the course is over.
Day 1: Intro to NGS, Linux and TACC
- Getting started at TACC – – logging inOverview NGS data processing, part 1 (2016_05
- more Getting started at TACC – setting up the environment
- Overview NGS data processing, part 2 (2016_05-NGSintro.pdf)
- more Getting started at TACC – file systems and transferring files
Day 2: NGS workflow overview and raw sequence pre-processing
- Overview NGS data processing, part 3 (2016_05-NGSintro.pdf)
- Running batch jobs at TACC
- Pre-processing raw sequences
Day 2: TACC batch system and FASTQ files
Day 3: Working with raw sequences
Day 4: Alignment and BAM file manipulation
- Overview NGS data processinglecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4 (2016_05)
- lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
5: Post-Alignment Analysis
- Samtools - viewing, counting and sorting your alignment data
- BedTools - analyzing your aligned dataFiltering with SAMTools
- Analysis using BEDTools