Pre-Workshop:
- Join the Slack Channel
- Read Pre-Workshop instructions
- Connect to the University of Idaho IBEST CRC servers
- Learn Unix command line via pre-recorded tutorials
- Set up for the live workshop (symlink to raw data)
Live Workshop:
Day 1 (Oct 30)
- Session 1 (8:30-10:30 PT, 9:30-11:30 MT):
- Introductions
- NGS sequencing technologies: Illumina, PacBio, ONT
- Illumina output
- NGS Applications Part 1: Whole genome sequencing
- Live coding: Illumina Fastq files
- Session 2 (2:00-4:00 PT, 3:00-5:00 MT):
- Live coding: Illumina whole genome sequence data
- Quality control
- Align to a reference genome
- Variant calling
- Live coding: Illumina whole genome sequence data
Day 2 (Nov 6)
- Session 1 (8:30-10:30 PT, 9:30-11:30 MT):
- NGS Applications Part 2
- RADseq
- DNA capture
- Amplicon sequencing
- RNAseq
- Epigenomics
- Low quality DNA
- How to choose a method
- Breakout groups
- NGS Applications Part 2
- Session 2 (2:00-4:00 PT, 3:00-5:00 MT):
- Computer resources available to GEM3
- Report back from breakout groups
- Live coding: Illumina whole genome sequence data
- Loops
- Filtering
- Bioinformatics Best Practices
- Other resources and skills you should learn
This workshop was made possible by the NSF Idaho EPSCoR Program and by the National Science Foundation under award number OIA-1757324.