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Comparison of de novo assembly statistics of Cucumis sativus L.
Author(s): Michał Wojcieszek; Wiktor Kuśmirek; Magdalena Pawełkowicz; Wojciech Pląder; Robert M. Nowak
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Paper Abstract

Genome sequencing is the core of genomic research. With the development of NGS and lowering the cost of procedure there is another tight gap - genome assembly. Developing the proper tool for this task is essential as quality of genome has important impact on further research. Here we present comparison of several de Bruijn assemblers tested on C. sativus genomic reads. The assessment shows that newly developed software - dnaasm provides better results in terms of quantity and quality. The number of generated sequences is lower by 5 - 33% with even two fold higher N50. Quality check showed reliable results were generated by dnaasm. This provides us with very strong base for future genomic analysis.

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, 1044533 (7 August 2017); doi: 10.1117/12.2280629
Show Author Affiliations
Michał Wojcieszek, Warsaw Univ. of Life Sciences (Poland)
Wiktor Kuśmirek, Warsaw Univ. of Technology (Poland)
Magdalena Pawełkowicz, Warsaw Univ. of Life Sciences (Poland)
Wojciech Pląder, Warsaw Univ. of Life Sciences (Poland)
Robert M. Nowak, 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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