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The efficient algorithm for mapping next generation sequencing reads to reference genome
Author(s): Patryk Pankiewicz; Wiktor Kuśmirek; Robert M. Nowak
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Paper Abstract

One of the main problem related to genomics is finding similarities between different species represented by DNA sequences. The dynamic programming algorithms (Needleman-Wunsch, Smith-Waterman) give a good measure of similarity, but are not efficient for big data sets. In this study we present the new heuristic algorithm based on common parts of reads. The approach can handle all types of sequencing errors: insertions, deletions and replacements. Our algorithm result is similar to other well known tools. The presented algorithm is implemented in C++, it uses Boost libraries, it internally use threads for parallel computing. This algorithm is a part of the DNA assembler ’dnaasm’. Source code, demo application and supplementary materials are available at project homepage: http://dnaasm.sourceforge.net.

Paper Details

Date Published: 6 November 2019
PDF: 7 pages
Proc. SPIE 11176, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2019, 111761W (6 November 2019); doi: 10.1117/12.2536653
Show Author Affiliations
Patryk Pankiewicz, Warsaw Univ. of Technology (Poland)
Wiktor Kuśmirek, Warsaw Univ. of Technology (Poland)
Robert M. Nowak, Warsaw Univ. of Technology (Poland)


Published in SPIE Proceedings Vol. 11176:
Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2019
Ryszard S. Romaniuk; Maciej Linczuk, Editor(s)

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