[REVIEW]: RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

[editorialbot]

Submitting author: !--author-handle-->@cagret<!--end-author-handle-- (Clement AGRET) Repository: https://gite.lirmm.fr/doccy/RedOak Branch with paper.md (empty if default branch): Version: v0.1.5 Editor: !--editor-->@lpantano<!--end-editor-- Reviewers: @swatimanekar, @samhorsfield96 Archive: 10.6084/m9.figshare.21711767

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@swatimanekar & @samhorsfield96, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @swatimanekar

📝 Checklist for @samhorsfield96

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bib/bbw089 is OK
- 10.1111/pbi.12499 is OK
- 10.1093/gigascience/giy125 is OK
- 10.1093/nar/gkp492 is OK
- 10.1186/1471-2105-12-242 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1137/070685531 is OK
- 10.1016/S0020-0255(01)00098-6 is OK
- 10.1007/978-3-642-39053-1_42 is OK
- 10.1109/DCC.2016.17 is OK
- 10.1093/bioinformatics/btu756 is OK
- 10.1093/bioinformatics/btv603 is OK
- 10.1186/s13015-016-0083-7 is OK
- 10.1093/bioinformatics/btw609 is OK
- 10.1137/0222058 is OK
- 10.1093/bioinformatics/btt460 is OK
- 10.1371/journal.pone.0109384 is OK
- 10.1186/s13015-016-0066-8 is OK
- 10.4230/OASIcs.GCB.2013.35 is OK
- 10.1186/s12864-017-4401-3 is OK
- 10.1089/cmb.2017.0258 is OK
- 10.1093/bioinformatics/btz162 is OK
- 10.1038/nature11346 is OK
- 10.1038/s41588-018-0041-z is OK
- 10.1038/sdata.2018.79 is OK
- 10.1186/2047-217X-3-8 is OK

MISSING DOIs

- 10.1007/978-3-540-30218-6_19 may be a valid DOI for title: Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation
- 10.1007/978-3-642-03784-9_7 may be a valid DOI for title: Compressed Suffix Arrays for Massive Data
- 10.1007/978-3-319-38851-9_22 may be a valid DOI for title: CHICO: A Compressed Hybrid Index for Repetitive Collections

INVALID DOIs

- None

[cagret]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "month" (NAME) [#<BibTeX::Bibliography data=[7]>, "@", #<BibTeX::Entry >, {:author=>["Edgar Gabriel and Graham E. Fagg and George Bosilca and Thara Angskun and Jack J. Dongarra and Jeffrey M. Squyres and Vishal Sahay and Prabhanjan Kambadur and Brian Barrett and Andrew Lumsdaine and Ralph H. Castain and David J. Daniel and Richard L. Graham and Timothy S. Woodall "], :title=>["Open {MPI}: Goals, Concept, and Design of a Next Generation {MPI} Implementation"], :booktitle=>["Proceedings, 11th European PVM/MPI Users' Group Meeting"], :year=>["2004"], :address=>["Budapest, Hungary"], :pages=>["97--104"], :doi=>["10.1007/978-3-540-30218-6_19"]}]

[cagret]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bib/bbw089 is OK
- 10.1111/pbi.12499 is OK
- 10.1093/gigascience/giy125 is OK
- 10.1093/nar/gkp492 is OK
- 10.1186/1471-2105-12-242 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1137/070685531 is OK
- 10.1007/978-3-540-30218-6_19 is OK
- 10.1016/S0020-0255(01)00098-6 is OK
- 10.1007/978-3-642-39053-1_42 is OK
- 10.1109/DCC.2016.17 is OK
- 10.1093/bioinformatics/btu756 is OK
- 10.1093/bioinformatics/btv603 is OK
- 10.1186/s13015-016-0083-7 is OK
- 10.1093/bioinformatics/btw609 is OK
- 10.1137/0222058 is OK
- 10.1093/bioinformatics/btt460 is OK
- 10.1371/journal.pone.0109384 is OK
- 10.1186/s13015-016-0066-8 is OK
- 10.1007/978-3-642-03784-9_7 is OK
- 10.4230/OASIcs.GCB.2013.35 is OK
- 10.1186/s12864-017-4401-3 is OK
- 10.1007/978-3-319-38851-9_22 is OK
- 10.1089/cmb.2017.0258 is OK
- 10.1093/bioinformatics/btz162 is OK
- 10.1038/nature11346 is OK
- 10.1038/s41588-018-0041-z is OK
- 10.1038/sdata.2018.79 is OK
- 10.1186/2047-217X-3-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cagret]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

@lpantano hi, I don't understand the error, with This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) it compiles without any error. If you can get help I'm interested. Thanks in advance

[samhorsfield96]

@swatimanekar I fixed all the review from the docx, except the square which indicates the end of the theorem. I didI did not regenerate the pdf. For the main review i don't understand "Given the non-dedicated tools like jellyfish and BFT, it's not completely clear to me that the time and memory as resource comparisons are fair", I only see time and RAM to compare tools that only use time and memory. Knowing that we have fixed the number of CPU, I'm not sure what else to do. Thank you very much for the feedback.

@samhorsfield96 I have made changes on the statement of need. Tell me if it's ok now.

@lpantano I think it's ok

Thank you very much everyone

Yes this looks good. I've updated the checklist.

[lpantano]

@samhorsfield96, can you check your list again? I see four items still unchecked: Functionality documentation, Automated tests, A statement of need,Quality of writing. Can you double check what is resolved for you again, and mention what is still need more work? I know you have pointed in previous comments your review, but since there has been many changes, it would be good to see a new comment with whatever is still unsolved. Thanks!

[lpantano]

@arfon we are having an issue with compiling the paper that the author can not reproduce, do you have any tips for this error? Thanks!

[cagret]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

i change \ell to 'l' maybe it can fix this.. PDF : "reduce the final score by ℓ−k/ℓ , whereas the percentage of identity is ℓ−1/ℓ . Latex : $\frac{\ell-k}{\ell}$, whereas the percentage of identity is $\frac{l-1}{l}$. new latex : $\frac{l-k}{l}$, whereas the percentage of identity is $\frac{l-1}{l}$.

[cagret]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

How can I see the files that are compiled by the latex? I have a feeling that they are not the right files.

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[samhorsfield96]

@lpantano @cagret There are a few things that I have noted in the automatically generated pdf and the repository:

• There are no automated tests, although there is a manual guide for checking the installation. However the expected output is missing in the repository https://gite.lirmm.fr/doccy/RedOak#:~:text=resources/makeRedOakQsubYaml.sh-,SGE%20command,-example%20obtained%20with
• The automatically generated pdf does not contain any figures detailing Redoak's implementation, or results when comparing to other tools. These are present in the BioRxiv version however.
• The heading for 'Example' contains a spelling error in the automatically generated pdf.
• In the BioRxiv version, the discussion contains results. These should be moved to the dedicated "Results" section.

I hope this helps. Let me know if you have any further questions.

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

i'll reduce the size of the structure

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lpantano]

Hi @swatimanekar, @samhorsfield96, @cagret,

@swatimanekar, I think the paper now contains the statement of need, can you check is enough for you for the current version. As well, What the authors will need to add to complete the functionality documentation?

@cagret, did you go over the last comments from @samhorsfield96?

@samhorsfield96, besides your previous comment, would be the last ones to check the following items: Automated test, State of the field, and Quality of writing?

Thanks everybody, we are in the final state of this review. Can you comment here on the different questions to each of you? Thanks!

[lpantano]

@cagret, I think it would be good if you could reduced the paper to 3-4 pages (not counting references). If you have a biorXiv, you can point to more detailed description to that link. Thanks!

[cagret]

Yes, I think I have been go over all the comments. Ok for the reduction, I will do that. Thanks again for everything.

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf

[cagret]

i reduced the number of pages

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[cagret]

@editorialbot generate pdf @lpantano now it'll fit.

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lpantano]

Hi @samhorsfield96, @swatimanekar, could you update the current status of your review after @cagret updated and worked on your comments? Thank you in advance.