De novo assembly of viral quasispecies using overlap graphs

• Published in: Genome research Vol. 27; no. 5; pp. 835 - 848
• Main Authors: Baaijens, Jasmijn A., Aabidine, Amal Zine El, Rivals, Eric, Schönhuth, Alexander
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.05.2017
• Subjects: Bioinformatics; Computer Science; Contig Mapping - methods; Contig Mapping - standards; Genome, Viral; Genomics - methods; Genomics - standards; Haplotypes; Hepacivirus - genetics; Method; Polymorphism, Genetic; Reference Standards; Sequence Analysis, DNA - methods; Sequence Analysis, DNA - standards; Software; Zika Virus - genetics; Virus; Software; Genomics/standards; Algorithm; Zika

A viral quasispecies, the ensemble of viral strains populating an infected person, can be highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection, determining the haplotypes of the individual strains can play a key role. As many viruses are subject to high mutation a...