This is the home of the Core NGS Tools course, May 2016June 2025, at https://utexas.atlassian.net/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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We will meet in Room 4.128 of Mezes Hall. We encourage you to use the computers provided in the classroom, but you may also use your personal laptops. |
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – – logging inOverview NGS data processing, part 1 (2016_05
- lecture: NGS overview & technology (2025_06-NGSintro.pdf, part 1)
- Setting up your TACC environmentOverview NGS data processing, part 2 (2016_05
- File systems and transferring files
Day 2: TACC batch system and FASTQ files
- lecture: NGS Terminology (2025_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (2025_06-NGSintro.pdf, part 3)
- File systems and transferring Working with FASTQ files
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3: Working with raw sequences
- lecture: Sequence QC & preparation (2025_06-NGSintro.pdf, part 3)
- Running batch jobs at TACC
- Pre-processing raw sequences
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Day 4: Alignment and BAM file manipulation
- Overview NGS data processinglecture: Alignment to a reference (2025_06-NGSintro.pdf, part 4 (2016_05)
- Alignment Overview and References
- lecture: Alignment to a reference (2025_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- More Alignment exercises
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5: Post-Alignment Analysis
- Samtools - viewing, counting and sorting your alignment data
- BedTools - analyzing your aligned dataFiltering with SAMTools
- Analysis using BEDTools
Resources
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