Signal-based optical map alignment.

In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with...

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Autores principales:	Mehmet Akdel, Henri van de Geest, Elio Schijlen, Irma M H van Rijswijck, Eddy J Smid, Gabino Sanchez-Perez, Dick de Ridder
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5b1890074b14452920ab733c5b1ad6f
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id	oai:doaj.org-article:e5b1890074b14452920ab733c5b1ad6f
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spelling	oai:doaj.org-article:e5b1890074b14452920ab733c5b1ad6f2021-12-02T20:07:57ZSignal-based optical map alignment.1932-620310.1371/journal.pone.0253102https://doaj.org/article/e5b1890074b14452920ab733c5b1ad6f2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253102https://doaj.org/toc/1932-6203In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available through http://www.bif.wur.nl/.Mehmet AkdelHenri van de GeestElio SchijlenIrma M H van RijswijckEddy J SmidGabino Sanchez-PerezDick de RidderPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0253102 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mehmet Akdel Henri van de Geest Elio Schijlen Irma M H van Rijswijck Eddy J Smid Gabino Sanchez-Perez Dick de Ridder Signal-based optical map alignment.
description	In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available through http://www.bif.wur.nl/.
format	article
author	Mehmet Akdel Henri van de Geest Elio Schijlen Irma M H van Rijswijck Eddy J Smid Gabino Sanchez-Perez Dick de Ridder
author_facet	Mehmet Akdel Henri van de Geest Elio Schijlen Irma M H van Rijswijck Eddy J Smid Gabino Sanchez-Perez Dick de Ridder
author_sort	Mehmet Akdel
title	Signal-based optical map alignment.
title_short	Signal-based optical map alignment.
title_full	Signal-based optical map alignment.
title_fullStr	Signal-based optical map alignment.
title_full_unstemmed	Signal-based optical map alignment.
title_sort	signal-based optical map alignment.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/e5b1890074b14452920ab733c5b1ad6f
work_keys_str_mv	AT mehmetakdel signalbasedopticalmapalignment AT henrivandegeest signalbasedopticalmapalignment AT elioschijlen signalbasedopticalmapalignment AT irmamhvanrijswijck signalbasedopticalmapalignment AT eddyjsmid signalbasedopticalmapalignment AT gabinosanchezperez signalbasedopticalmapalignment AT dickderidder signalbasedopticalmapalignment
_version_	1718375274322591744

Signal-based optical map alignment.

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