Abstract

Of the four species of influenza viruses (Influenza A-D), Influenza A is the most virulent in human hosts and subtypes of it have been responsible for all historic flu pandemics.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?
• Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses?
• How can we obtain meaningful phylogenetic insight from AIV consensus sequences?

Learning Objectives

• Determine how reassortment impacts reference-based mapping approaches
• Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping
• Construct a sample consensus genome from mapped reads
• Generate per-segment phylogenetic trees of AIV consensus sequences