Skip to content

Advertisement

Archived Comments for: Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Back to article

  1. khmer version & citation clarification

    Michael Crusoe, University of California, Davis

    23 November 2015

    There is no version 0.2 of khmer; we suspect that the authors used version 2.0, as that matches their citation. We appreciate the citation of our software though we request that both the software and the matching algorithm paper be cited.

    The authors did not specify which script in khmer was run, but by context we presume it was `normalize-by-median.py`, therefore the corresponding algorithm citation is "CT Brown et al., arXiv:1203.4802 [q-bio.GN]" as specified in the documentation and the "--help" output of that script.

    Finally we would like to highlight a formatting error concerning the command line options used as one of the dashes was replaced by an "em" dash. The correct formatting of the options to normalize-by-median.py is "-K 20 -C 20" or "--ksize 20 --cutoff 20" if using the long versions of the parameter names.

    Competing interests

    I was the lead developer of khmer from version 0.6 through to version 0.8.
  2. Response to the previous comment 'khmer version & citation clarification'

    Shigehiro Kuraku, RIKEN Center for Life Science Technologies

    14 December 2015

    Thank you very much for your comment and information.

    We wrote in the Methods the version (='0.2') included in the file README.html of the khmer package, as the source code did not include any version record. We thank you for indicating to us that the version included in the file README.html was not updated. We have checked the date of our package download and the release log at GitHub, which revealed that the version used in the paper was most likely 0.7.1.

    We also appreciate your pointing out that we failed to include the exact name of the script in the khmer package used in this study. It was ‘normalize_by_median.py’.

    For readers’ information, I include here the link to the algorithm citation you suggest: http://arxiv.org/abs/1203.4802

    Competing interests

    I am the corresponding author of this research article.
  3. More acknowledgements

    Shigehiro Kuraku, RIKEN Center for Life Science Technologies

    14 December 2015

    As we realized that the section Acknowledgements in our article was not complete, we here acknowledge Juan Pascual Anaya and Nathalie Feiner who commented on an earlier version of the manuscript and Miyuki Noro who assisted gecko embryo sampling, for their valuable contributions.

    Competing interests

    I am the corresponding author of this research article.

Advertisement