This is the home of the Core NGS Tools course, May 2018, 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.
We will meet in Room 206 of Parlin hall (PAR). As there are no workstations available in this room, you will need to bring your personal laptop or work closely with someone who has one.
There will be a ~15 minute break each day around 10:30am with refreshments available in PAR 303.
Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (2017_05-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: Working with raw sequences
- TACC overview
- lecture: the FASTQ format (2017_05-NGSintro.pdf, part 2)
- Working with FASTQ files
- lecture: Sequence QC & preparation (2017_05-NGSintro.pdf, part 3)
- Sequence quality control with FastQC
Day 3: Alignment and BAM file manipulation
- TACC batch jobs
- Trimming sequences
- lecture: Alignment to a reference (2017_05-NGSintro.pdf, part 4)
- Alignment
