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Katome: de novo DNA assembler implemented in rust
Author(s): Łukasz Neumann; Robert M. Nowak; Wiktor Kuśmirek
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Paper Abstract

Katome is a new de novo sequence assembler written in the Rust programming language, designed with respect to future parallelization of the algorithms, run time and memory usage optimization. The application uses new algorithms for the correct assembly of repetitive sequences. Performance and quality tests were performed on various data, comparing the new application to `dnaasm', `ABySS' and `Velvet' genome assemblers. Quality tests indicate that the new assembler creates more contigs than well-established solutions, but the contigs have better quality with regard to mismatches per 100kbp and indels per 100kbp. Additionally, benchmarks indicate that the Rust-based implementation outperforms `dnaasm', `ABySS' and `Velvet' assemblers, written in C++, in terms of assembly time. Lower memory usage in comparison to `dnaasm' is observed.

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, 104451D (7 August 2017); doi: 10.1117/12.2280206
Show Author Affiliations
Łukasz Neumann, Warsaw Univ. of Technology (Poland)
Robert M. Nowak, Warsaw Univ. of Technology (Poland)
Wiktor Kuśmirek, 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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