This is the home of the Core NGS Tools course, June 20212022, 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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This workshop will be held via Zoom, URL: For online attendees, the Zoom URL is: https://utexas.zoom.us/j/9196514176198995501041 There will be a short break each day around 10:30am. Your TACC account will remain on our class' class TACC project allocation through June 30, 2021. | ||
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2022 We will provide Contact us for access to recordings of each day's materials after the course is over (links will be removed from this page).
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20212022_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 (20212022_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (20212022_06-NGSintro.pdf, part 3)
- Working with FASTQ files
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- lecture: Sequence QC & preparation (20212022_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
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- lecture: Alignment to a reference (20212022_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- lecture: Alignment to a reference (20212022_06-NGSintro.pdf, part 4)
- More Alignment exercises
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Resources
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