Katome: de novo DNA assembler implemented in rust

Łukasz Neumann; Robert M. Nowak; Wiktor Kuśmirek

doi:10.1117/12.2280206

7 August 2017 Katome: de novo DNA assembler implemented in rust

Łukasz Neumann, Robert M. Nowak, Wiktor Kuśmirek

Proceedings Volume 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017; 104451D (2017) https://doi.org/10.1117/12.2280206
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2017, 2017, Wilga, Poland

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.

Citation Download Citation

Łukasz Neumann, Robert M. Nowak, and Wiktor Kuśmirek "Katome: de novo DNA assembler implemented in rust", Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 104451D (7 August 2017); https://doi.org/10.1117/12.2280206

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