[PRE REVIEW]: Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.

[editorialbot]

Submitting author: !--author-handle-->@JeanMainguy<!--end-author-handle-- (Jean Mainguy) Repository: https://github.com/genotoul-bioinfo/Binette Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @lskatz, @beardymcjohnface Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @JeanMainguy. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (535.9 files/s, 69877.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            948            579           1871
Markdown                        10            249              0            458
TeX                              1             25              0            184
YAML                             6             40             46            171
TOML                             1              7              4             57
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            36           1281            637           2776
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 850

[editorialbot]

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

OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK

MISSING DOIs

- 10.1038/s41592-018-0046-7 may be a valid DOI for title: Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[luizirber]

@editorialbot assign me as editor

[editorialbot]

Assigned! @luizirber is now the editor

[JeanMainguy]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/s41592-018-0046-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[JeanMainguy]

Here are some suggestions for potential reviewers:

• beardymcjohnface
• Robaina
• mdehollander
• MmasterT
• telatin

[JeanMainguy]

@editorialbot generate preprint

[editorialbot]

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

[JeanMainguy]

Hello @luizirber Just a quick follow-up regarding the reviewer search for my submission. Is there anything I can do to help ? Thanks Jean

[JeanMainguy]

Hi @luizirber

Binette submission seems to be stuck in pre-review. Is there anything I can do to move it forward? In the meantime, I've uploaded Binette to BioRxiv (https://www.biorxiv.org/content/10.1101/2024.04.20.585171v1).

Thanks!

[arfon]

@editorialbot assign me as editor

:wave: @JeanMainguy – I'm sorry it has taken so long to get this submission moving. I'll pick this up from here.

[editorialbot]

Assigned! @arfon is now the editor

[arfon]

@lskatz, @oschwengers, @beardymcjohnface, @Robaina, @mdehollander – :wave: would any of you be willing to review this submission for JOSS? The submission under consideration is Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, and past submissions to JOSS, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

[beardymcjohnface]

Happy to review!

[lskatz]

Sign me up! I know less python and so if there is a better reviewer, please defer to them.

[arfon]

Amazing, thanks both! I'll add you now and get the review started.

[arfon]

@editorialbot add @lskatz as reviewer

[editorialbot]

@lskatz added to the reviewers list!

[arfon]

@editorialbot add @beardymcjohnface as reviewer

[editorialbot]

@beardymcjohnface added to the reviewers list!

[arfon]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6782.

[arfon]

@lskatz, @beardymcjohnface, @JeanMainguy – see you all over in #6782 where the actual review will take place