Content of review 1, reviewed on January 05, 2015

Major Revisions

  1. The analysis of this paper relies on alignments generated with BLASR. They found that only a minority reads aligned to the known amplicon reference (10-20%). It has been shown that BLASR is not appropriate alignment method for minion data with LASTZ increasing the number of aligned reads of 1D data by ~50X and 2D data by ~ 10X (http://www.homolog.us/blogs/blog/2014/09/09/loman-and-browns-nanopore-presentation-live-feed/). As the authors analysis relies on the total number of bases aligned to each reference this is likely to be underpowered with this method. They should repeat the analysis using the appropiate tool.

  2. The metric of sum of length of all alignments needs to be explored with another analysis. I would like to see also an attempt to derive a consensus, or at least average identity to each reference.

Level of interest An article whose findings are important to those with closely related research interests Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interest

Source

    © 2015 the Reviewer (CC BY 4.0 - source).

Content of review 2, reviewed on February 15, 2015

The authors present a much improved manuscript with my major compulsory revisions met.

Minor Essential Revisions

  1. Misspelling MinION as MinIO in introduction
  2. Line 127 – Sentence doesn’t make sense. “ The MinION reads generally represent to the complete length of the ...“
  3. Line 189 Missing a “0”? of .51 to 2.04

Level of interest An article whose findings are important to those with closely related research interests Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests

Source

    © 2015 the Reviewer (CC BY 4.0 - source).

References

    Andy, K., L., H. J., J., C. E., T., L. A., L., W. K., R., K. D., Nicole, R. C., S., M. S. 2015. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. GigaScience.