Core NGS Tools Home

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.

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

• Filtering with SAMTools
• Analysis using BEDTools

Resources

• Linux fundamentals
• Some Linux commands

• Core NGS Resources

• Decimal and Hexadecimal
• Data wrangling best practices