Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data

Bolognini, Davide and Magi, Alberto (2021) Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data. Frontiers in Genetics, 12. ISSN 1664-8021

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Abstract

Structural variants (SVs) are genomic rearrangements that involve at least 50 nucleotides and are known to have a serious impact on human health. While prior short-read sequencing technologies have often proved inadequate for a comprehensive assessment of structural variation, more recent long reads from Oxford Nanopore Technologies have already been proven invaluable for the discovery of large SVs and hold the potential to facilitate the resolution of the full SV spectrum. With many long-read sequencing studies to follow, it is crucial to assess factors affecting current SV calling pipelines for nanopore sequencing data. In this brief research report, we evaluate and compare the performances of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. In particular, we focus on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges and provide insights into precision and recall of SV callsets generated by integrating the various long-read aligners and SV callers. The computational pipeline we propose is publicly available at https://github.com/davidebolo1993/EViNCe and can be adjusted to further evaluate future nanopore sequencing datasets.

Item Type: Article
Subjects: Open Archive Press > Medical Science
Divisions: Faculty of Engineering, Science and Mathematics > School of Chemistry
Faculty of Engineering, Science and Mathematics > School of Civil Engineering and the Environment
Faculty of Engineering, Science and Mathematics > School of Electronics and Computer Science
Faculty of Engineering, Science and Mathematics > School of Engineering Sciences
Depositing User: Unnamed user with email support@openarchivepress.com
Date Deposited: 27 Jan 2023 06:35
Last Modified: 04 Apr 2024 09:33
URI: http://library.2pressrelease.co.in/id/eprint/275

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