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CBRS Summer School: Genome Variant Analysis

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.

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Jun 20, 2022 - Jun 24, 2022
9:00 am - 11:30 am