hands-on tutorial
Hands-on for 'Avian influenza viral strain analysis from gene segment sequencing data' tutorial
The questions this addresses are:
- 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?
The objectives are:
- 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
Licence: Creative Commons Attribution 4.0 International
Keywords: variant-analysis, virology
Target audience: Students
Resource type: hands-on tutorial
Contributors: Wolfgang Maier
Scientific topics: Genetic variation
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