This is the home of the Core NGS Tools course, June 20202021, 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.
There will be a ~10 minute 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 in
- Setting up your TACC environment
- File systems and transferring files
TACC batch system and FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation ( 2020
- 2021_06-NGSintro.pdf, part 3)
- Sequence quality control
4: Alignment and BAM file manipulation
- lecture: Alignment to a reference ( 2020
- 2021_06-NGSintro.pdf, part 4)
- lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
Day 5: Post-Alignment Analysis
Day 5: Miscellaneous
- Catch up from previous days