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 flow variation graph, capturing all quasispecies diversity present in the sample. VG-Flow computes a solution to the contig abundance estimation problem and employs a greedy algorithm to efficiently build full-length haplotypes. Finally, VG-Flow calculates accurate frequency estimates for the reconstructed haplotypes through linear programming techniques.

Evolutionary Intelligence

Baaijens, J.A, Stougie, L, & Schönhuth, A. (2018). VG-flow: haplotype reconstruction and abundance estimation from mixed samples using flow variation graphs.