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.

Details

Title
NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing
Author
Cheng Yong Tham; Tirado-Magallanes, Roberto; Goh, Yufen; Fullwood, Melissa J; Bryan T.H. Koh; Wang, Wilson; Ng, Chin Hin; Chng, Wee Joo; Thiery, Alexandre; Tenen, Daniel G; Touati Benoukraf
Pages
1-15
Section
Software
Publication year
2020
Publication date
2020
Publisher
BioMed Central
ISSN
14747596
e-ISSN
1474760X
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2379042195
Copyright
© 2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.