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Open Access

De Novo Assembly Methods for Next Generation Sequencing Data

Yiming He, Zhen Zhang, Xiaoqing Peng, Fangxiang Wu, Jianxin Wang( )
School of Information Science and Engineering, Central South University, Changsha 410083, China
Morehouse School of Medicine, Atlanta, GA 30310, USA
Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
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Abstract

The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454, Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet, SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.

Keywords

next-generation sequencinggenome assemblyoverlap/lapout/consensusde Bruijn graph

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Tsinghua Science and Technology
Volume 18 Issue 5,
October 2013
Pages 500-514
DOI: 10.1109/TST.2013.6616523
Cite this article:
He Y, Zhang Z, Peng X, et al. De Novo Assembly Methods for Next Generation Sequencing Data. Tsinghua Science and Technology, 2013, 18(5): 500-514. https://doi.org/10.1109/TST.2013.6616523

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Received: 09 August 2013
Revised: 24 August 2013
Accepted: 25 August 2013
Published: 03 October 2013
© The author(s) 2013
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