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Tsinghua Science and Technology 2013, 18(5): 500-514 https://doi.org/10.1109/TST.2013.6616523
Open Access | Issue | Published: 03 October 2013

De Novo Assembly Methods for Next Generation Sequencing Data

Show Author's Information 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
Keywords:
next-generation sequencing, genome assembly, overlap/lapout/consensus, de Bruijn graph
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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Abstract Full text About this article

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.


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About this article

De Novo Assembly Methods for Next Generation Sequencing Data

Show Author's information 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

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 sequencing, genome assembly, overlap/lapout/consensus, de Bruijn graph

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Received: 09 August 2013
Revised: 24 August 2013
Accepted: 25 August 2013
Published: 03 October 2013
Issue date: October 2013

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© The author(s) 2013

Acknowledgements

This work was supported in part by the National Natural Science Foundation of China (Nos. 61232001, 61128006, and 61073036).

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