Comparison of de novo assembly statistics of Cucumis sativus L.

Michał Wojcieszek; Wiktor Kuśmirek; Magdalena Pawełkowicz; Wojciech Pląder; Robert M. Nowak

doi:10.1117/12.2280629

7 August 2017 Comparison of de novo assembly statistics of Cucumis sativus L.

Michał Wojcieszek, Wiktor Kuśmirek, Magdalena Pawełkowicz, Wojciech Pląder, Robert M. Nowak

Proceedings Volume 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017; 1044533 (2017) https://doi.org/10.1117/12.2280629
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2017, 2017, Wilga, Poland

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.

Citation Download Citation

Michał Wojcieszek, Wiktor Kuśmirek, Magdalena Pawełkowicz, Wojciech Pląder, and Robert M. Nowak "Comparison of de novo assembly statistics of Cucumis sativus L.", Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 1044533 (7 August 2017); https://doi.org/10.1117/12.2280629

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