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: 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.