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Variant Detection Using Galaxy

This workshop will cover the concepts of detection small variants, including SNPs and small indels, from next-generation sequencing data. You will use and compare a number of popular variant detection tools, visualise variants using a genome browser, and annotate SNPs for predicted biological effects.


The workshop will all be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools.


Recommended Participants

Biologists and other life scientists planning to work with next-generation sequencing data for small variant detection. 


Learning Objectives

  • Perform QC evaluation and filtering on next-generation sequencing data

  • Select and use relevant variant detection software and apply appropriate quality filters to screen variants

  • View variant and sequence data using the Integrative Genomics Viewer (IGV)

  • Carry out preliminary functional annotation of predicted variants


Syllabus

  • Access and use of the Galaxy bioinformatics analysis platform

  • Quality control and filtering of next-generation sequencing data

  • Next-generation sequencing read mapping

  • Visualisation of mapped reads with the Integrative Genomics Viewer

  • Use of and comparison of software applications to call genomic variants

  • Filtering and screening protocols to generate lists of high-confidence SNPs

  • Initial annotation of the predicted biological impact of identified variants

Upcoming workshops

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