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NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.

ABSTRACT: The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we present NanoVar, an optimized structural variant caller utilizing low-depth (8X) whole-genome sequencing data generated by Oxford Nanopore Technologies. NanoVar exhibits higher structural variant calling accuracy when benchmarked against current tools using low-depth simulated datasets. In patient samples, we successfully validate structural variants characterized by NanoVar and uncover normal alternative sequences or alleles which are present in healthy individuals.

SUBMITTER: Tham CY

PROVIDER: S-EPMC7055087 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.

Tham Cheng Yong CY Tirado-Magallanes Roberto R Goh Yufen Y Fullwood Melissa J MJ Koh Bryan T H BTH Wang Wilson W Ng Chin Hin CH Chng Wee Joo WJ Thiery Alexandre A Tenen Daniel G DG Benoukraf Touati T

Genome biology 20200303 1

The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we present NanoVar, an optimized structural variant caller utilizing low-depth (8X) whole-genome sequencing data generated by Oxford Nanopore Technologies. NanoVar exhibits higher structural variant cal ...[more]

PMID: 32127024

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