This is the home of the Core NGS Tools course, June 2024, 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.

For online attendees, the Zoom URL is: https://utexas.zoom.us/j/99997003778
There will be a short break each day around 10:30am
We will provide access to recordings of each day's materials after the course is over
Your TACC account will remain on our class TACC project allocation through June 30, 2024

Day 1: Intro to NGS, Linux and TACC

Introduction
Getting started at TACC – logging in
lecture: NGS overview & technology (2024_06-NGSintro.pdf, part 1)
Setting up your TACC environment
File systems and transferring files

Day 2: TACC batch system and FASTQ files

lecture: NGS Terminology (2024_06-NGSintro.pdf, part 2)
TACC batch jobs
lecture: the FASTQ format (2024_06-NGSintro.pdf, part 3)
Working with FASTQ files

Day 3: Working with raw sequences

lecture: Sequence QC & preparation (2024_06-NGSintro.pdf, part 3)
Sequence quality control
Trimming

Day 4: Alignment and BAM file manipulation

lecture: Alignment to a reference (2024_06-NGSintro.pdf, part 4)
Alignment Overview and References
lecture: Alignment to a reference (2024_06-NGSintro.pdf, part 4)
The Basic Alignment Workflow
More Alignment exercises

Day 5: Post-Alignment Analysis

Resources

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