De Novo DNA assembler for third generation sequencers’ reads based on BLASR algorithm

Michał Winiarski , Wiktor Kuśmirek , Robert Marek Nowak

Abstract

The most significant differences between second and third sequencing generation are length of reads and percentage of errors. In the field of de novo DNA assembly there is a need for new effective algorithms as these used for second generation reads are highly ineffective or even unusable when applied to the successor. In this article we propose a solution tailored for DNA assembly of reads from third generation sequencers. In this approach we use overlap-layout-consensus (OLC) graph method. It is composed of number of algorithms focusing on time and memory optimization. The proposed algorithm was implemented as shared library and added as a new module to the ’dnaasm’ de novo assembler. The implementation has been tested on simulated as well as real data. Results prove increase in speed and memory consumption in comparison with other de novo DNA assemblers.
Author Michał Winiarski (FEIT / ICS)
Michał Winiarski,,
- The Institute of Computer Science
, Wiktor Kuśmirek (FEIT / IN)
Wiktor Kuśmirek,,
- The Institute of Computer Science
, Robert Marek Nowak (FEIT / IN)
Robert Marek Nowak,,
- The Institute of Computer Science
Pages108083C-1-108083C-9
Publication size in sheets0.5
Book Romaniuk Ryszard, Linczuk Maciej Grzegorz (eds.): Proceedings of SPIE: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, Proceedings of SPIE: The International Society for Optical Engineering, vol. 10808, 2018, SPIE - the International Society for Optics and Photonics, ISBN 9781510622036, 2086 p., DOI:10.1117/12.2504983
Keywords in EnglishDNA assembler, de novo assembling, third-generation sequencing, computer program, overlap consensus graph
DOIDOI:10.1117/12.2501542
URL https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10808/2501542/De-Novo-DNA-assembler-for-third-generation-sequencers-reads-based/10.1117/12.2501542.full?SSO=1
projectDevelopment of new algorithms in the areas of software and computer architecture, artificial intelligence and information systems and computer graphics . Project leader: Arabas Jarosław, , Phone: +48 22 234 7432, start date 01-08-2018, planned end date 31-12-2018, II/2018/DS/1, Implemented
WEiTI Działalność statutowa
Languageen angielski
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108083C_kusmirek.pdf 797.24 KB
Score (nominal)15
ScoreMinisterial score = 15.0, 16-04-2019, BookChapterSeriesAndMatConf
Ministerial score (2013-2016) = 15.0, 16-04-2019, BookChapterSeriesAndMatConf
Publication indicators WoS Citations = 0
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