Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall.

ABSTRACT: Advances in long-read sequencing (LRS) technology continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo genome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant calling precision and recall of Oxford Nanopore Technologies (ONT) and PacBio HiFi platforms over a range of sequence coverages. For read-based

SUBMITTER: Harvey WT 

PROVIDER: S-EPMC10187267 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature