This is the home of the Core NGS Tools course, May 2015June 2023, 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 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
Day 2: NGS workflow overview and raw sequence pre-processing
- Overview NGS data processing
Pre-processing raw sequencesPDF name NGSinfro.pdf - Overview NGS data processing
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
- Samtools - viewing, counting and sorting your alignment data
- BedTools - analyzing your aligned data – logging in
- lecture: NGS overview & technology (2023_06-NGSintro.pdf part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: TACC batch 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 (2023_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation (2023_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day 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 (2023_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5: Post-Alignment Analysis
Resources
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