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The low cost and high throughput of next generation sequencing provides an unprecedented opportunity to assay variability within the genomes of individuals and populations. Using the Galaxy platform, we will explore the new generation of aligners built specifically for the demands of high throughput sequences, and walk through the GATK Best Practices pipeline for SNP and indel calling using Illumina sequences. In addition, we will cover the use of variant effect prediction software such as SnpEff, and visualize the predicted variants in their genomic context using the UCSC Genome Browser.

Students should have some familiarity with both the Galaxy platform and next generation sequencing technologies; attendance of our “Introduction to Next Generation Sequence Analysis with Galaxy” or equivalent experience is recommended.