Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Section: New Software and Platforms


Viral haplotype reconstruction from contigs using variation graphs

Keyword: Haplotyping

Functional Description: Viruses populate their hosts as a viral quasispecies: a collection of genetically related mutant strains. Viral quasispecies assembly refers to reconstructing the strain-specific haplotypes from read data, and predicting their relative abundances within the mix of strains, an important step for various treatment-related reasons. Reference-genome-independent (de novo) approaches have yielded benefits over reference-guided approaches, because reference-induced biases can become overwhelming when dealing with divergent strains. While being very accurate, extant de novo methods only yield rather short contigs. Virus-VG aims to reconstruct full-length haplotypes together with their abundances from such contigs, represented as a genome variation graph.