Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data

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...

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Autores principales:	Davide Bolognini , Alberto Magi
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	bioinformatics nanopore sequencing genomics structural variation long reads Genetics QH426-470
Acceso en línea:	https://doaj.org/article/0dad08f6f6014de693dd7f26a30db70f
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spelling	oai:doaj.org-article:0dad08f6f6014de693dd7f26a30db70f2021-11-18T08:30:15ZEvaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data1664-802110.3389/fgene.2021.761791https://doaj.org/article/0dad08f6f6014de693dd7f26a30db70f2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.761791/fullhttps://doaj.org/toc/1664-8021Structural 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.Davide Bolognini Alberto Magi Frontiers Media S.A.articlebioinformaticsnanopore sequencinggenomicsstructural variationlong readsGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics nanopore sequencing genomics structural variation long reads Genetics QH426-470
spellingShingle	bioinformatics nanopore sequencing genomics structural variation long reads Genetics QH426-470 Davide Bolognini Alberto Magi Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
description	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.
format	article
author	Davide Bolognini Alberto Magi
author_facet	Davide Bolognini Alberto Magi
author_sort	Davide Bolognini
title	Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
title_short	Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
title_full	Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
title_fullStr	Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
title_full_unstemmed	Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data
title_sort	evaluation of germline structural variant calling methods for nanopore sequencing data
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0dad08f6f6014de693dd7f26a30db70f
work_keys_str_mv	AT davidebolognini evaluationofgermlinestructuralvariantcallingmethodsfornanoporesequencingdata AT albertomagi evaluationofgermlinestructuralvariantcallingmethodsfornanoporesequencingdata
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Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data

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