HQAlign: Aligning nanopore reads for SV detection using current-level modeling.

ABSTRACT:

Motivation

Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate alignment of these long reads play an important role in identifying novel SVs. Long read sequencers such as nanopore sequencing can address this problem by providing very long reads but with high error rates, making accurate alignment challenging. Many errors induced by nanopore sequencing have a bias because of the physics of the sequencing process and proper utilization of these error characteristics can play an important role in designing a robust aligner for SV detection problems. In this paper, we design and evaluate HQAlign, an aligner for SV dete

SUBMITTER: Joshi D 

PROVIDER: S-EPMC9882582 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature