This is the home of the Core NGS Tools course, June 20222024, at https://wikisutexas.utexasatlassian.edunet/wiki/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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Your TACC account will remain on our class TACC project allocation through June 30, 2022
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20222024_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
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- lecture: NGS Terminology (20222024_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (20222024_06-NGSintro.pdf, part 3)
- Working with FASTQ files
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- lecture: Sequence QC & preparation (20222024_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
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- lecture: Alignment to a reference (20222024_06-NGSintro.pdf, part 4)
- The Basic Alignment WorkflowOverview and References
- lecture: Alignment to a reference (20222024_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- More Alignment exercises
Day 5: Post-Alignment Analysis
Resources
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