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Proceedings Paper

New tool to assemble repetitive regions using next-generation sequencing data
Author(s): Wiktor Kuśmirek; Robert M. Nowak; Łukasz Neumann
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Paper Abstract

The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

Paper Details

Date Published: 7 August 2017
PDF: 8 pages
Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 104452V (7 August 2017); doi: 10.1117/12.2280030
Show Author Affiliations
Wiktor Kuśmirek, Warsaw Univ. of Technology (Poland)
Robert M. Nowak, Warsaw Univ. of Technology (Poland)
Łukasz Neumann, Warsaw Univ. of Technology (Poland)


Published in SPIE Proceedings Vol. 10445:
Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017
Ryszard S. Romaniuk; Maciej Linczuk, Editor(s)

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