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Scaffolding of long read assemblies using long range contact information

Jay Ghurye, Mihai Pop, Sergey Koren, Chen-Shan Chin
doi: https://doi.org/10.1101/083964
Jay Ghurye
1Department of Computer Science, University of Maryland, College Park, 20740, USA
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Mihai Pop
1Department of Computer Science, University of Maryland, College Park, 20740, USA
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Sergey Koren
2National Human Genome Research Institute, Bethesda, USA 21702
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Chen-Shan Chin
3Pacific Biosciences, Menlo Park, 94025, USA
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Abstract

Motivation Long read technologies have made a revolution in de novo genome assembly by generating contigs of size orders of magnitude more than that of short read assemblies. Although the assembly contiguity has increased, it still does not span a chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scalable and computationally efficient scaffolding method that can boost the contiguity of the assembly by a large extent using genome wide chromatin interaction data such as Hi-C. Particularly, we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies.

Results We tested our methods on two long read assemblies of different organisms. We compared our method with previously developed method and show that our approach performs better in terms of accuracy of scaffolding.

Availability The software is available for free use and can be downloaded from here: https://github.com/machinegun/hi-c-scaffold

Contact jchin{at}pacificbiosciences.com

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-NC-ND 4.0 International license.
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Posted October 27, 2016.
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Scaffolding of long read assemblies using long range contact information
Jay Ghurye, Mihai Pop, Sergey Koren, Chen-Shan Chin
bioRxiv 083964; doi: https://doi.org/10.1101/083964
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Scaffolding of long read assemblies using long range contact information
Jay Ghurye, Mihai Pop, Sergey Koren, Chen-Shan Chin
bioRxiv 083964; doi: https://doi.org/10.1101/083964

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