Skip to main content

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

The Original Article was published on 27 December 2012


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].


  1. Luo R et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:18.

    Article  PubMed  PubMed Central  Google 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”.

Download references

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Tak-Wah Lam or Jun Wang.

Additional information

Ruibang Luo, Binghang Liu, Yinlong Xie and Zhenyu Li contributed equally to this work.

The online version of the original article can be found under doi:10.1186/2047-217X-1-18.

Rights and permissions

Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

To view a copy of this licence, visit

The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Luo, R., Liu, B., Xie, Y. et al. Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaSci 4, 30 (2015).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: