This is the home of the Core NGS Tools course, June 2020, 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
Day 2: Working with raw sequences
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
Day 5: Miscellaneous
- Catch up from previous days