Section: New Software and Platforms

VG-Flow

Viral haplotype reconstruction from contigs using variation graphs

Keyword: Haplotyping

Functional Description: The goal of haplotype-aware genome assembly is to reconstruct all individual haplotypes from a mixed sample and to provide corresponding abundance estimates. VG-flow provides a reference-genome-independent solution based on the construction of a variation graph, capturing all quasispecies diversity present in the sample. We solve the contig abundance estimation problem and propose a greedy algorithm to efficiently build full-length haplotypes. Finally, we obtain accurate frequency estimates for the reconstructed haplotypes through linear programming techniques.

• Contact: Alexander Schonhuth

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