This is the home of the Core NGS Tools course, May 2018June 2023, 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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We meet in Room 206 of Parlin hall (PAR). As there are no workstations available in this room, you will need to bring your personal laptop or work closely with someone who has one. You will also need a UT EID to access the UT wireless network.
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology ( 2017
- 2023_ 05
- 06-NGSintro.pdf ,
- part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: TACC batch
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system and FASTQ files
- Catch up day 1 TACC setup
- lecture: NGS Terminology (2023_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (20172023_0506-NGSintro.pdf, part 23)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation (20172023_0506-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming sequences
Day
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4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2023_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- lecture: Alignment to a reference ( 2017
- 2023_ 05
- 06-NGSintro.pdf, part 4)
- More Alignment exercises
Day
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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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