Genome Variant Analysis (THIS COURSE IS CLOSED)
- June 14 - June 18
- 9:00 am - 11:30 am
- Daniel Deatherage, Ph.D. (Postdoctoral Research Associate, Molecular Biosciences)
Course Closes: June 7
Description: This course is designed to teach you how to identify genomic variants from a variety of NGS library sources (mixed populations, whole genome, enriched/targeted panels, rare variant, amplicon, etc.) for both prokaryotic and eukaryotic organisms. The course emphasizes using existing data sources to allow participants to analyze real data in the same step-by-step manner that one would analyze their own data. The modular nature of exercises allows participants of all computational skill levels to benefit from both instruction and hands-on practice in areas they are personally most interested in while providing introductory resources to analysis types they may encounter in the future. Additional lecture/discussion will focus on understanding strengths and weaknesses of different sequencing library types, alternative analysis programs, different sequencing platforms, and how to best utilize TACC resources and existing pipelines to make analysis faster. Major data analysis steps include: sequencing quality assessment and improvement, obtaining or constructing reference genomes, read mapping, variant calling, visualization and reporting. Using programs and pipelines such as: FastQC, MultiQC, cutadapt, Trimmomatic, SPAdes, Unicycler, SAMtools, Bowtie2, bedtools, breseq, IGV, and GATK.
Instructor Bio: Daniel Deatherage earned his doctorate at The Ohio State University studying epigenetic effects of ovarian cancer. His postdoctoral work in Dr. Jeffrey Barrick’s lab has focused on using next generation sequencing to identify ultra rare mutations within evolving populations and diagnose synthetic biology constructs failure modes. In general, he is interested in using next generation sequencing to answer novel questions that may not be answerable by other methods.
Preferred or Prerequisite Skills: None
Computer Requirement: Students must use their own laptops. TACC Account and UT EID are required. Please be sure you know both your UT EID and your TACC username when you come to class. To obtain a UT EID, go here. To sign up for a TACC account, go here.
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