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Authors: Yuki Endo 1 ; Fubito Toyama 1 ; Chikafumi Chiba 2 ; Hiroshi Mori 1 and Kenji Shoji 1

Affiliations: 1 Utsunomiya University, Japan ; 2 University of Tsukuba, Japan

ISBN: 978-989-758-012-3

Keyword(s): Bioinfomatics, Next Generation Sequencing, De Novo Assembly

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Next Generation Sequencing ; Sequence Analysis

Abstract: Determining whole genome sequences of various species has many applications not only in biological system, but also in medicine, pharmacy and agriculture. In recent years, the emergence of high-throughput next generation sequencing technologies has dramatically reduced time and costs for whole genome sequencing. These new technologies provide ultrahigh throughput with lower unit data cost. However, the data are very short length fragments of DNA. Thus, developing algorithms for merging these fragments is very important. Merging these fragments without reference data is called de novo assembly. Many algorithms for de novo assembly have been proposed in recent years. Velvet, one of the algorithms, is famous because it has good performance in terms of memory and time consumption. But memory consumption increases dramatically when the size of input fragments is huge. Therefore, it is necessary to develop algorithm with low memory usage. In this paper, we propose an algorithm for de novo assembly with lower memory. In our experiments using E.coli K-12 strain MG 1655, memory consumption of the proposed algorithm was one-third of that of Velvet. (More)

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Paper citation in several formats:
Endo, Y.; Toyama, F.; Chiba, C.; Mori, H. and Shoji, K. (2014). De Novo Short Read Assembly Algorithm with Low Memory Usage.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 215-220. DOI: 10.5220/0004881002150220

@conference{bioinformatics14,
author={Yuki Endo. and Fubito Toyama. and Chikafumi Chiba. and Hiroshi Mori. and Kenji Shoji.},
title={De Novo Short Read Assembly Algorithm with Low Memory Usage},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={215-220},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004881002150220},
isbn={978-989-758-012-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - De Novo Short Read Assembly Algorithm with Low Memory Usage
SN - 978-989-758-012-3
AU - Endo, Y.
AU - Toyama, F.
AU - Chiba, C.
AU - Mori, H.
AU - Shoji, K.
PY - 2014
SP - 215
EP - 220
DO - 10.5220/0004881002150220

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