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

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.Ministry of Education (MOE)National Research Foundation (NRF)Published versionWork in the T.B. laboratory is supported by the National Research Foundation, the Singapore Ministry of Education under its Centres of Excellence initiative and the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education’s AcRF Tier 3 grants [MOE2014-T3-1-006]. This research was undertaken, in part, thanks to funding from the Canada Research Chairs program. C.Y.T. and R.T.M. are supported by a Doctoral Scholarship from the Cancer Science Institute of Singapore