MiniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data.

ABSTRACT: Nanopore sequence technology has demonstrated a longer read length and enabled to potentially address the limitations of short-read sequencing including long-range haplotype phasing and accurate variant calling. However, there is still room for improvement in terms of the performance of single nucleotide variant (SNV) identification and computing resource usage for the state-of-the-art approaches. In this work, we introduce miniSNV, a lightweight SNV calling algorithm that simultaneously achieves high performance and yield. miniSNV utilizes known common variants in populations as variation backgrounds and leverages read pileup, read-based phasing, and consensus generation to identify and genotype SNVs for Oxford Nanopore Technologies (ONT) long reads. Benchmarks on real and simulated ONT d

SUBMITTER: Cui M 

PROVIDER: S-EPMC11428505 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature