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1 October 2018 De Novo DNA assembler for third generation sequencers’ reads based on BLASR algorithm
Michał Winiarski, Wiktor Kuśmirek, Robert M. Nowak
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Proceedings Volume 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018; 108083C (2018) https://doi.org/10.1117/12.2501542
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 2018, Wilga, Poland
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.
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Michał Winiarski, Wiktor Kuśmirek, and Robert M. Nowak "De Novo DNA assembler for third generation sequencers’ reads based on BLASR algorithm", Proc. SPIE 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 108083C (1 October 2018); https://doi.org/10.1117/12.2501542
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KEYWORDS
Computer science
Software
Algorithms
Bioinformatics
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