This is the home of the Core NGS Tools course, May 2014June 2022, 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.
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We will meet in Room 101B of the Flawn Academic Center (FAC) building. We encourage you to use the computers provided in the classroom, but you may also use your personal laptops. |
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For online attendees, the Zoom URL is: https://utexas.zoom.us/j/98995501041 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, 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 (2022_06-NGSintro.pdf part 1)
- Setting up your TACC environment
- File systems and transferring files
- Catch up day 1 TACC setup
Day 2: TACC batch system and FASTQ files
- Catch up day 1 TACC setup
- lecture: NGS Terminology (2022_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (2022_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation (2022_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5: Post-Alignment Analysis
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Day 1: Linux and TACC
- Introduction
- Overview NGS data processing
- Getting started at TACC
Day 2: NGS workflow overview and raw sequence pre-processing
- Running batch jobs at TACC
- Finish – Overview NGS data processing
- Start – Pre-processing FASTQ sequences
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
- Samtools - viewing, counting and sorting your alignment data
- Analyzing your aligned experiment with BedTools Odds and ends
Resources
- Linux fundamentals
Core NGS Tools -- Resource lists
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