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A Reference Bacterial Genome Dataset Generated on the Miniontm Portable Single-Molecule Nanopore Sequencer Joshua Quick1,2, Aaron R Quinlan3 and Nicholas J Loman1*

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A Reference Bacterial Genome Dataset Generated on the Miniontm Portable Single-Molecule Nanopore Sequencer Joshua Quick1,2, Aaron R Quinlan3 and Nicholas J Loman1* Quick et al. GigaScience (2015) 4:6 DOI 10.1186/s13742-015-0043-z ERRATUM Open Access Erratum: A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer Joshua Quick1,2, Aaron R Quinlan3 and Nicholas J Loman1* Recently we noticed that we could not reproduce Author details Figure three (Figure 1 here) while analysing this data as 1Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. 2NIHR Surgical Reconstruction and Microbiology part of a new experiment [1]. This was due to a modifica- Research Centre, University of Birmingham, B15 2TT, Birmingham, UK. 3Center tion to the script used for extracting sequence alignment for Public Health Genomics, University of Virginia, Virginia, Charlottesville, VA profiles from the dataset [2]. On further investigation we 22908, US. found that an error in this script had been reported and Received: 31 December 2014 Accepted: 5 January 2015 a fix supplied by an anonymous online contributor on October 27th 2014 via Github [3]. The error prevented mismatches from being properly counted in the calcu- References lation of read accuracy (insertions and deletions were). 1. Quick J, Quinlan AR, Loman NJ. A reference bacterial genome dataset generated on the minion™ portable single-molecule nanopore We therefore present updated versions of Figures three sequencer. GigaScience. 2014;3:22. (Figure 1 here) and four (Figure 2 here) generated by the 2. Quinlan AR. 2014. https://github.com/arq5x/nanopore-scripts/blob/ corrected script. We are grateful to the anonymous con- master/count-errors.py.Github 3. Anon. 2014. https://github.com/arq5x/nanopore-scripts/pull/1.Github tributor who noticed this error. The manuscript text and tables are unaffected. We would also like to correct the spelling of Minh Duc Cao in the Acknowledgements section. We apologise for any inconvenience caused by this error. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar *Correspondence: [email protected] • Research which is freely available for redistribution 1Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK Submit your manuscript at Full list of author information is available at the end of the article www.biomedcentral.com/submit © 2015 Quick et al.; licensee BioMed Central. 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. Quick et al. GigaScience (2015) 4:6 Page 2 of 3 R7 (LAST −q1) R7 (LAST -q2) 0.3 0.2 0.1 0.0 R7.3 (LAST -q1) R7.3 (LAST −q2) 0.3 density 0.2 0.1 0.0 60 70 80 90 60 70 80 90 Percent identity Template Complement Normal 2D Full 2D Figure 1 Kernel density plots showing accuracy for R7 and R7.3 chemistries with two different values for the LAST substitution penalty score. Quick et al. GigaScience (2015) 4:6 Page 3 of 3 Template Complement Normal 2D Full 2D 1.00 0.75 R7−q1 0.50 0.25 0.00 1.00 0.75 R7−q2 0.50 0.25 0.00 1.00 0.75 Fraction of read aligned Fraction R73−q1 0.50 0.25 0.00 1.00 0.75 R73−q2 0.50 0.25 0.00 10 30 50 70 90 10 30 50 70 90 10 30 50 70 90 10 30 50 70 90 Percent identity Figure 2 Alignment identity and completeness. Each plot reflects the alignment identity and the proportion of the read aligned for all 2D reads, as well as the underlying template and complement sequences. The top two panels reflect the alignment results for normal and full 2D reads from the R7 flowcell, and the bottom two panels reflect the R7.3 flowcell. Left panels employ a mismatch penalty of 1 and right panels reflect a mismatch penalty of 2. Overall, the lower mismatch penalty increases the identity and fraction of the read that aligned and this effect is greatest for full 2D reads..
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