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Hybrid correction of highly noisy Oxford Nanopore long reads using a variable-order de Bruijn graph

Pierre Morisse, Thierry Lecroq, Arnaud Lefebvre
doi: https://doi.org/10.1101/238808
Pierre Morisse
1Normandie Univ, UNIROUEN, LITIS, 76000 Rouen, France
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Thierry Lecroq
1Normandie Univ, UNIROUEN, LITIS, 76000 Rouen, France
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Arnaud Lefebvre
1Normandie Univ, UNIROUEN, LITIS, 76000 Rouen, France
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Abstract

Motivation The recent rise of long read sequencing technologies such as Pacific Biosciences and Oxford Nanopore allows to solve assembly problems for larger and more complex genomes than what allowed short reads technologies. However, these long reads are very noisy, reaching an error rate of around 10 to 15% for Pacific Biosciences, and up to 30% for Oxford Nanopore. The error correction problem has been tackled by either self-correcting the long reads, or using complementary short reads in a hybrid approach, but most methods only focus on Pacific Biosciences data, and do not apply to Oxford Nanopore reads. Moreover, even though recent chemistries from Oxford Nanopore promise to lower the error rate below 15%, it is still higher in practice, and correcting such noisy long reads remains an issue.

Results We present HG-CoLoR, a hybrid error correction method that focuses on a seed-and-extend approach based on the alignment of the short reads to the long reads, followed by the traversal of a variable-order de Bruijn graph, built from the short reads. Our experiments show that HG-CoLoR manages to efficiently correct Oxford Nanopore long reads that display an error rate as high as 44%. When compared to other state-of-the-art long read error correction methods able to deal with Oxford Nanopore data, our experiments also show that HG-CoLoR provides the best trade-off between runtime and quality of the results, and is the only method able to efficiently scale to eukaryotic genomes.

Availability and implementation HG-CoLoR is implemented is C++, supported on Linux platforms and freely available at https://github.com/morispi/HG-CoLoR

Contact: pierre.morisse2{at}univ-rouen.fr

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 22, 2017.
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Hybrid correction of highly noisy Oxford Nanopore long reads using a variable-order de Bruijn graph
Pierre Morisse, Thierry Lecroq, Arnaud Lefebvre
bioRxiv 238808; doi: https://doi.org/10.1101/238808
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Hybrid correction of highly noisy Oxford Nanopore long reads using a variable-order de Bruijn graph
Pierre Morisse, Thierry Lecroq, Arnaud Lefebvre
bioRxiv 238808; doi: https://doi.org/10.1101/238808

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