2022 Core NGS Tools Home

This is the home of the Core NGS Tools course, June 2022, 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

• 2022 Introduction
• 2022 Getting started at TACC – logging in
• lecture: NGS overview & technology (2022_06-NGSintro.pdf part 1)
• Setting up your TACC environment
• 2022 File systems and transferring files
• 2022 Catch up day 1 TACC setup

Day 2: TACC batch system and FASTQ files

• 2022 Catch up day 1 TACC setup
• lecture: NGS Terminology (2022_06-NGSintro.pdf, part 2)
• TACC batch jobs
• lecture: the FASTQ format (2022_06-NGSintro.pdf, part 3)
• 2022 Working with FASTQ files

Day 3: Working with raw sequences

• lecture: Sequence QC & preparation (2022_06-NGSintro.pdf, part 3)
• Sequence quality control
• Trimming

Day 4: Alignment and BAM file manipulation

• lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
• 2022 The Basic Alignment Workflow
• lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
• 2022 More Alignment exercises

Day 5: Post-Alignment Analysis

• 2022 Filtering with SAMTools
• 2022 Analysis using BEDTools

Resources

• 2022 Linux fundamentals

• 2022 Core NGS Resources

• 2022 Decimal and Hexadecimal
• 2022 Data wrangling best practices