Viral quasispecies reconstruction via contig abundance estimation in variation graphs

Viral quasispecies assembly aims to reconstruct all mutant strains populating an infected patient and to provide corresponding abundance estimates. We provide 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. Our method outperforms state-of-the-art approaches in viral quasispecies assembly and has the potential to assemble bacterial genomes in a strain aware manner as well.