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Proceedings Paper

Scaffolding algorithm using second- and third-generation reads
Author(s): Wiktor Franus; Wiktor Kuśmirek; Robert M. Nowak
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Paper Abstract

The second generation sequencing methods produce high-quality short reads, which are assembled into contigs by DNA assemblers. Due to the fact that length of a single read is limited to 500bp it is really hard to assembly full genomes or full chromosomes. Generating longer contigs with low cost of sequencing is a main effort of computer scientists in this area. We propose to link contings created from second-generation reads using reads from third-generation sequencers. Such reads have length 10-20kbp. An existing implementation of this approach appears to be time and memory demanding for larger genomes. We developed an algorithm based on Bloom filter and extremely memory-efficient associative array. Our implementation remarkably exceeds the previous one in terms of time and memory consumption. Presented algorithm, provided as a shared library, is a part of the dnaasm de-novo assembler. The library has been created using C++ programming language, Boost and Google Sparse Hash libraries. Both web browser-based graphical user interface and command line interface are provided. Source code as well as a demo web application and a docker image are available at the dnaasm project web-page: Our application has been tested on real data of bacteria, yeast and plant genomes.

Paper Details

Date Published: 1 October 2018
PDF: 10 pages
Proc. SPIE 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 108083A (1 October 2018); doi: 10.1117/12.2501505
Show Author Affiliations
Wiktor Franus, Warsaw Univ. of Technology (Poland)
Wiktor Kuśmirek, Warsaw Univ. of Technology (Poland)
Robert M. Nowak, Warsaw Univ. of Technology (Poland)

Published in SPIE Proceedings Vol. 10808:
Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018
Ryszard S. Romaniuk; Maciej Linczuk, Editor(s)

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