Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement.

ABSTRACT:

Background

After an infection, human cells may contain viral genomes in the form of episomes or integrated DNA. Comparing the genomic sequences of different strains of a virus in human cells can often provide useful insights into its behaviour, activity and pathology, and may help develop methods for disease prevention and treatment. To support such comparative analyses, the viral genomes need to be accurately reconstructed from a large number of samples. Previous efforts either rely on customized experimental protocols or require high similarity between the sequenced genomes and a reference, both of which limit the general applicability of these approaches. In this study, we propose a pipeline, named ASPIRE, for reconstructing viral genomes accurately from short reads data of huma

SUBMITTER: Lee SD 

PROVIDER: S-EPMC9169298 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature