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Title
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Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome
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Author
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Abstract
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| We sequenced the genome of the Yoruban reference individual NA19240 on the long-read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, as well as a comparison with the performance of structural variant calling from short-read sequencing data. The structural variant caller Sniffles after NGMLR or minimap2 alignment provides the most accurate results, but additional confidence or sensitivity can be obtained by a combination of multiple variant callers. Sensitive and fast results can be obtained by minimap2 for alignment and a combination of Sniffles and SVIM for variant identification. We describe a scalable workflow for identification, annotation, and characterization of tens of thousands of structural variants from long-read genome sequencing of an individual or population. By discussing the results of this well-characterized reference individual, we provide an approximation of what can be expected in future long-read sequencing studies aiming for structural variant identification. |
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Language
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English
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Source (journal)
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Genome research. - Cold Spring Harbor, N.Y., 1995, currens
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Publication
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Cold Spring Harbor, N.Y.
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2019
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ISSN
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1088-9051
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DOI
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10.1101/GR.244939.118
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Volume/pages
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29
:7
(2019)
, p. 1178-1187
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ISI
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000473730600013
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Pubmed ID
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31186302
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Full text (Publisher's DOI)
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Full text (publisher's version - intranet only)
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