Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

ABSTRACT: High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based a

SUBMITTER: Morse AM 

PROVIDER: S-EPMC5580483 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature