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This is the home of the Core NGS Tools course, June 2021, 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.

Day 1: Intro to NGS, Linux and TACC

• Introduction
• Getting started at TACC – logging in
• lecture: NGS overview & technology (2020_06-NGSintro.pdf, part 1)
• Setting up your TACC environment

Day 2: Transferring files and TACC

• File systems and transferring files
• lecture: NGS Terminology (2020_06-NGSintro.pdf, part 2)
• TACC batch jobs

Day 3: Working with raw sequences

• lecture: the FASTQ format (2020_06-NGSintro.pdf, part 3)
• Working with FASTQ files
• lecture: Sequence QC & preparation (2020_06-NGSintro.pdf, part 3)
• Sequence quality control
• Trimming

Day 4: Alignment and BAM file manipulation

• lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
• The Alignment workflow – references
• lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
• The Alignment workflow – performing an alignment

Day 5: Post-Alignment Analysis

• Filtering with SAMTools
• Analysis using BEDTools

Resources

• Linux fundamentals

• Core NGS Resources

• Data wrangling best practices