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Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić
doi: https://doi.org/10.1101/068122
Robert Vaser
1Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, Unska 3, 10000 Zagreb, Croatia
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Ivan Sović
2Centre for Informatics and Computing, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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Niranjan Nagarajan
3Genome Institute of Singapore, Singapore 138672, Singapore
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Mile Šikić
1Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, Unska 3, 10000 Zagreb, Croatia
4Bioinformatics Institute, Singapore 138671, Singapore
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  • For correspondence: mile.sikic@fer.hr
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Abstract

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

Racon is available open source under the MIT license at https://github.com/isovic/racon.git.

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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 4.0 International license.
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Posted August 05, 2016.
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Fast and accurate de novo genome assembly from long uncorrected reads
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić
bioRxiv 068122; doi: https://doi.org/10.1101/068122
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Fast and accurate de novo genome assembly from long uncorrected reads
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić
bioRxiv 068122; doi: https://doi.org/10.1101/068122

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