Open AccessViral quasispecies reconstruction via tensor factorization with successive read removal
Author(s) -
Soyeon Ahn,
Ziqi Ke,
Haris Vikalo
Publication year - 2018
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/bty291
Subject(s) - viral quasispecies , biology , computational biology , strain (injury) , population , inference , genetics , computer science , algorithm , genome , artificial intelligence , gene , demography , sociology , anatomy
As RNA viruses mutate and adapt to environmental changes, often developing resistance to anti-viral vaccines and drugs, they form an ensemble of viral strains--a viral quasispecies. While high-throughput sequencing (HTS) has enabled in-depth studies of viral quasispecies, sequencing errors and limited read lengths render the problem of reconstructing the strains and estimating their spectrum challenging. Inference of viral quasispecies is difficult due to generally non-uniform frequencies of the strains, and is further exacerbated when the genetic distances between the strains are small.