Preprint reviews by Minh Duc Cao

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

Aaron Quinlan, Josh Quick, Nicholas Loman

Review posted on 06th October 2014

Comments to the author

Quick et al present a read dataset from the much anticipated Nanopore sequencing platform. They sequenced the model organism E. coli K12 MG1655 genome with two latest chemistries R7 and R7.3 and performed an analysis of the two resulted sets of data. The data are provided in native FAST5 format.

I find the introduction of the dataset is valuable to the research community in a timely manner. There are many speculations, anticipations and discussions of Nanopore sequencing technology around with limited data available. This whole genome sequencing dataset will give the research community access to real Nanopore sequencing data, and will no doubt facilitate the development of bioinformatics methods to analyse Nanopore data.

Major Compulsory Revisions

None.

Minor Essential Revisions

  1. The authors need to make clear whether the numbers of template and complement reads reported include those that are turned into 2D reads (page 4, para 3).

  2. The annotations of the two Figures are hardly readable. The colour choice of Figure 2 makes it hard to interpret, especially for R7. The authors should increase the font size of the two Figures, and have a better colour scheme for Figure 2.

  3. The last sentence of Abstract, Background: I would argue that the MinION device measures the change of current which can be used to deduce the nucleotide sequence, but it does not deduce the nucleotide sequence.

  4. The last sentence of Abstract, Findings: remove "and" between "second" and "one."

  5. Line 4, page 4 should read:``reconised by an abasic site which produces a..." (add s to produce).

  6. Line 5, page 4 should read: ``The complement strand is slowed down by a second enzyme termed the HP motor" (insert by). In fact, the term HP motor should be introduced earlier in the manuscript, especially before the descriptions of R7 and R7.3 library preparation (page 2).

Discretionary Revisions:

  1. The authors describe data from two runs using R7 and R7.3 chemistries in the manuscript. They also make available two extra datasets from the modified R7 protocol which significantly increases the relative number of full 2D reads. It would be more valuable to include a description and an analysis of these two datasets in the manuscript.

  2. I would be interested to see the report of the fraction of reads that are aligned (or equivalently, not aligned), and an analysis of alignment of template/complement reads that are not turned to 2D reads.

Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests: I declare that I have no competing interests.

Disclaimer: I am also part of the Oxford Nanopore MinION Access Program (MAP).

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A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

Aaron Quinlan, Josh Quick, Nicholas Loman

Review posted on 29th September 2014

Quick et al present a read dataset from the much anticipated Nanopore sequencing platform. They sequenced the model organism E. coli K12 MG1655 genome with two latest chemistries R7 and R7.3 and performed an analysis of the two resulted sets of data. The data are provided in native FAST5 format.


I find the introduction of the dataset is valuable to the research community in a timely manner. There are many speculations, anticipations and discussions of Nanopore sequencing technology around with limited data available. This whole genome sequencing dataset will give the research community access to real Nanopore sequencing data, and will no doubt facilitate the development of bioinformatics methods to analyse Nanopore data.


Major Compulsory Revisions
None.

Minor Essential Revisions

1. The authors need to make clear whether the numbers of template and complement reads reported include those that are turned into 2D reads (page 4, para 3).

2. The annotations of the two Figures are hardly readable. The colour choice of Figure 2 makes it hard to interpret, especially for R7. The authors should increase the font size of the two Figures, and have a better colour scheme for Figure 2.

3. The last sentence of Abstract, Background: I would argue that the MinION device measures the change of current which can be used to deduce the nucleotide sequence, but it does not deduce the nucleotide sequence.

4. The last sentence of Abstract, Findings: remove "and" between "second" and "one."

5. Line 4, page 4 should read:``reconised by an abasic site which produces a..." (add s to produce).

6. Line 5, page 4 should read: ``The complement strand is slowed down by a second enzyme termed the HP motor" (insert by). In fact, the term HP motor should be introduced earlier in the manuscript, especially before the descriptions of R7 and R7.3 library preparation (page 2).

Discretionary Revisions:
1. The authors describe data from two runs using R7 and R7.3 chemistries in the manuscript. They also make available two extra datasets from the modified R7 protocol which significantly increases the relative number of full 2D reads. It would be more valuable to include a description and an analysis of these two datasets in the manuscript.

2. I would be interested to see the report of the fraction of reads that are aligned (or equivalently, not aligned), and an analysis of alignment of template/complement reads that are not turned to 2D reads.

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Given your assessment of the manuscript, what do you advise should be the next step?: Accept after minor essential revisions

Please indicate how interesting you found the manuscript: An article of importance in its field

Quality of written English: Acceptable

Quality of Figures: Acceptable (with some improvements needed -- see comments).

Statistical review. Is it essential that this manuscript is seen by an expert statistician? If so, please give your reasons in your report: Yes, and I have assessed the statistics in my report.

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:

Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript?
Do you have any other financial competing interests?
Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I declare that I have no competing interests
===============================================================================
Disclaimer: I am also part of the Oxford Nanopore MinION Access Program (MAP).

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