VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.

ABSTRACT: RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring diversity from error-prone reads is challenging. Here, we present VILOCA (VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data), a method for mutation calling and reconstruction of local haplotypes from short- and long-read viral sequencing data. Local haplotypes refer to genomic regions that have approximately the length of the input reads. VILOCA recovers local haplotypes by using a Dirichlet process mixture model to cluster reads around their unobserved haplotypes and leveraging quality scores of the

SUBMITTER: Fuhrmann L 

PROVIDER: S-EPMC11616694 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature