This is the home of the Core NGS Tools course, June 2020, 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.
This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91282159612. Please make sure your version of Zoom is at least 5.0 (see https://zoom.its.utexas.edu/zoom-upgrade).
There will be a short break each day around 10:30am.
Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (2020_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
Recording of Day 1 (with audio transcript):
Day 2: Transferring files and TACC
- File systems and transferring files
- lecture: NGS Terminology (2020_06-NGSintro.pdf, part 2)
- TACC batch jobs
- Recording of Day 2 (with audio transcript):
Day 3: Working with raw sequences
- lecture: the FASTQ format (2020_06-NGSintro.pdf, part 3)
- Working with FASTQ files
- lecture: Sequence QC & preparation (2020_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
- Recording of Day 3 (with audio transcript):
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
- The Alignment workflow
