Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- Ruibang Luo†1, 2,
- Binghang Liu†1, 2,
- Yinlong Xie†1, 2, 3,
- Zhenyu Li†1, 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
Received: 15 June 2015
Accepted: 15 June 2015
Published: 8 July 2015
The original article was published in GigaScience 2012 1:18
Erratum
- 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.
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.
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.
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
References
- Luo R et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:18.View ArticlePubMedPubMed CentralGoogle Scholar
- 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.
- 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
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.
