Open Access

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

  • Ruibang Luo1, 2,
  • Binghang Liu1, 2,
  • Yinlong Xie1, 2, 3,
  • Zhenyu Li1, 2,
  • Weihua Huang1,
  • Jianying Yuan1,
  • Guangzhu He1,
  • Yanxiang Chen1,
  • Qi Pan1,
  • Yunjie Liu1,
  • Jingbo Tang1,
  • Gengxiong Wu1,
  • Hao Zhang1,
  • Yujian Shi1,
  • Yong Liu1,
  • Chang Yu1,
  • Bo Wang1,
  • Yao Lu1,
  • Changlei Han1,
  • David W. Cheung2,
  • Siu-Ming Yiu2,
  • Shaoliang Peng4,
  • Zhu Xiaoqian4,
  • Guangming Liu4,
  • Xiangke Liao4,
  • Yingrui Li1, 2,
  • Huanming Yang1,
  • Jian Wang1,
  • Tak-Wah Lam2Email author and
  • Jun Wang1Email author
Contributed equally
GigaScience20154:30

https://doi.org/10.1186/s13742-015-0069-2

Received: 15 June 2015

Accepted: 15 June 2015

Published: 8 July 2015

The original article was published in GigaScience 2012 1:18

Erratum

After the publication of ‘SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012 1:18’ [1] this paper was used as case study by the ISA, Research Object and Nanopublication communities to use their data models to try to quantitatively assess the reproducibility of published research. While the supporting data and overall results were found to be accurate, a number of semantic problems were detected in a few points of interpretation, and in order to ensure the accuracy of the scientific we now outline these in this correction article.
  1. 1.

    While there are huge improvements to the quality of the resulting assemblies, other than the tables it was not stressed in the text that the speed of SOAPdenovo2 can be slightly slower than SOAPdenovo v1.

     
  2. 2.

    In the testing an assessment section (page 3), based on the correct results in table 1, where we say the scaffold N50 metric is an order of magnitude longer from SOAPdenovo2 versus SOAPdenovo1, this was actually 45 times longer.

     
  3. 3.

    Also in the testing an assessment section, based on the correct results in table 1, where we say SOAPdenovo2 produced a contig N50 1.53 times longer than ALLPATHS-LG, this should be 2.18 times longer.

     
  4. 4.

    Finally in this section, where we say the correct assembly length produced by SOAPdenovo2 was 3–80 fold longer than SOAPdenovo1, this should be 3–64 fold longer.

     

To see more about how these errors were detected see the case study article [2]. To access all the supporting materials, ISA metadata and pipelines implemented in Galaxy to test these results on your own, please see the supporting entry in GigaDB [3].

Notes

Authors’ Affiliations

(1)
BGI HK Research Institute
(2)
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong
(3)
School of Bioscience and Bioengineering, South China University of Technology
(4)
School of Computer Science, National University of Defense Technology

References

  1. Luo R et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:18.View ArticlePubMedPubMed CentralGoogle Scholar
  2. González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M, Thompson M, et al. (2015) From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PLoS ONE 10(7): e0127612. doi:10.1371/journal.pone.0127612.
  3. 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 D, Yiu SM, Liu G, Zhu X, Peng S, Li Y, Yang H, Wang J, Lam TW, Wang J: Software and supporting material for “SOAPdenovo2: an empirically improved memory-efficient short read de novo assembly”. http://dx.doi.org/10.5524/100044.

Copyright

© Luo et al. 2015

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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