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OptiDiff: structural variation detection from single optical mapping reads

View ORCID ProfileMehmet Akdel, Dick de Ridder
doi: https://doi.org/10.1101/2022.01.08.475501
Mehmet Akdel
1Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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  • For correspondence: mehmet.akdel@wur.nl
Dick de Ridder
1Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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Abstract

Detecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/akdel/OptiDiff

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 11, 2022.
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OptiDiff: structural variation detection from single optical mapping reads
Mehmet Akdel, Dick de Ridder
bioRxiv 2022.01.08.475501; doi: https://doi.org/10.1101/2022.01.08.475501
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OptiDiff: structural variation detection from single optical mapping reads
Mehmet Akdel, Dick de Ridder
bioRxiv 2022.01.08.475501; doi: https://doi.org/10.1101/2022.01.08.475501

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