This is the home of the Core NGS Tools course, June 20202022, 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.
| Tip |
|---|
This workshop will be held via Zoom, URLFor online attendees, the Zoom URL is: 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).98995501041 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, 2022 We will provide access to recordings of each day's materials after the course is over. |
Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20202022_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
Recording of Day 1:
Day 2: Working with raw sequences
Day 2: TACC batch system and FASTQ files
- Catch up day 1 TACC setup
- lecture: NGS Terminology ( 2020
- 2022_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (20202022_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation ( 2020
- 2022_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day
...
4: Alignment and BAM file manipulation
- lecture: Alignment to a reference ( 2020
- 2022_06-NGSintro.pdf, part 4)
- The Alignment workflow
...
- Basic Alignment Workflow
- lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5: Post-Alignment Analysis
Day 5: Miscellaneous
- Catch up from previous days
Resources
...