2020 Core NGS Tools Home
This is the home of the Core NGS Tools course, June 2020, 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.
This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91282159612.
There will be a short break each day around 10:30am.
Contact us for access to recordings of each day's materials.
Day 1: Intro to NGS, Linux and TACC
2020 Getting started at TACC – logging in
lecture: NGS overview & technology (2020_06-NGSintro.pdf, part 1)
Day 2: Transferring files and TACC
lecture: NGS Terminology (2020_06-NGSintro.pdf, part 2)
Day 3: Working with raw sequences
lecture: the FASTQ format (2020_06-NGSintro.pdf, part 3)
lecture: Sequence QC & preparation (2020_06-NGSintro.pdf, part 3)
Day 4: Alignment and BAM file manipulation
lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
The 2020 Alignment workflow – references
lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
The 2020 Alignment workflow – performing an alignment