Section: New Software and Platforms

Virus-VG

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.

• Contact: Alexander Schonhuth

• URL: https://bitbucket.org/jbaaijens/virus-vg