Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.

ABSTRACT: Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencing of clinical specimens requires the accurate assembly of individual strains or sequence variants and suitable variant calling methods. However, the performance of most methods has not been assessed for populations composed of low divergent viral strains with large genomes, such as HCMV. In an extensive benchmarking study, we evaluated 15 assemblers and 6 variant callers on 10 lab-generated benchmark data sets created with two different library preparation protocols, to identify best practices and challenges for analyzing such data. Most assemblers, espec

SUBMITTER: Deng ZL 

PROVIDER: S-EPMC8138829 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature