Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications.

ABSTRACT: The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)-sequence differences between paralogous sequences-to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the pe

SUBMITTER: Prodanov T 

PROVIDER: S-EPMC7641771 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature