Introduction

BACKGROUND: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. FINDINGS: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. CONCLUSIONS: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Publications

  1. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
    Cite this
    Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J, 2012-01-01 - GigaScience

Credits

  1. Ruibang Luo
    Developer

    BGI HK Research Institute, 16 Dai Fu Street

  2. Binghang Liu
    Developer

  3. Yinlong Xie
    Developer

  4. Zhenyu Li
    Developer

  5. Weihua Huang
    Developer

  6. Jianying Yuan
    Developer

  7. Guangzhu He
    Developer

  8. Yanxiang Chen
    Developer

  9. Qi Pan
    Developer

  10. Yunjie Liu
    Developer

  11. Jingbo Tang
    Developer

  12. Gengxiong Wu
    Developer

  13. Hao Zhang
    Developer

  14. Yujian Shi
    Developer

  15. Yong Liu
    Developer

  16. Chang Yu
    Developer

  17. Bo Wang
    Developer

  18. Yao Lu
    Developer

  19. Changlei Han
    Developer

  20. David W Cheung
    Developer

  21. Siu-Ming Yiu
    Developer

  22. Shaoliang Peng
    Developer

  23. Zhu Xiaoqian
    Developer

  24. Guangming Liu
    Developer

  25. Xiangke Liao
    Developer

  26. Yingrui Li
    Developer

  27. Huanming Yang
    Developer

  28. Jian Wang
    Developer

  29. Tak-Wah Lam
    Developer

  30. Jun Wang
    Investigator

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Summary
AccessionBT006218
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByJun Wang