Pre-Workshop:

1. Join the Slack Channel
2. Read Pre-Workshop instructions
3. Connect to the University of Idaho IBEST CRC servers
4. Learn Unix command line via pre-recorded tutorials
5. Set up for the live workshop (symlink to raw data)

Live Workshop:

Day 1 (Oct 30)

1. 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
2. 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

Day 2 (Nov 6)

1. 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
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.}