[PRE REVIEW]: Corekaburra: pan-genome post-processing using core gene synteny

[editorialbot]

Submitting author: !--author-handle-->@milnus<!--end-author-handle-- (Magnus Jespersen) Repository: https://github.com/milnus/Corekaburra Branch with paper.md (empty if default branch): main Version: v0.0.4 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @iferres, @asafpr Managing EiC: Kevin M. Moerman

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Author instructions

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

@milnus if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (212.0 files/s, 58333.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          13            911            762           4053
Bourne Shell                     3             73             40            327
TeX                              1             16              0            168
Markdown                         2             37              0            119
YAML                             4              3              4             81
Dockerfile                       1              2              2              5
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SUM:                            24           1042            808           4753
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gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK

MISSING DOIs

- None

INVALID DOIs

- doi.org/10.1186/s13059-020-02090-4 is INVALID because of 'doi.org/' prefix

[editorialbot]

Wordcount for paper.md is 539

[editorialbot]

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

[milnus]

Reviewer suggestions from current reviewer list karinlag asafpr giraola

Reviewer suggestions not currently reviewing for JOSS: nzmacalasdair oschwengers harry-thorpe ggautreau

[Kevin-Mattheus-Moerman]

@milnus can you check the above invalid DOI :point_up: ? You can call @editorialbot check references to check these again, and you can call @editorialbot generate pdf to update the paper.

[Kevin-Mattheus-Moerman]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[milnus]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1186/s13059-020-02090-4 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[milnus]

@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:

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

👋🏻 @milnus - I will handle your submission, and start by finding two suitable reviewers (thanks for the suggestions above!)

[csoneson]

👋🏻 @karinlag, @asafpr, @giraola - would (two of) you be interested in reviewing this submission for JOSS?

Corekaburra: pan-genome post-processing using core gene synteny

[giraola]

I am out-of-office right now, but I think @iferres can be interested in having a look at it.

El jue, 3 nov 2022 a las 15:39, Charlotte Soneson @.***>) escribió:

👋🏻 @karinlag https://github.com/karinlag, @asafpr https://github.com/asafpr, @giraola https://github.com/giraola - would (two of) you be interested in reviewing this submission for JOSS?

Corekaburra: pan-genome post-processing using core gene synteny

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4889#issuecomment-1302522997, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD7JICLYGX4EGCQQ7DLTZILWGQBFRANCNFSM6AAAAAARRG3D7A . You are receiving this because you were mentioned.Message ID: @.***>

--

Gregorio Iraola, Ph.D.

Group Leader Microbial Genomics Lab http://iraola-lab.com Institut Pasteur Montevideo Mataojo 2020, Montevideo, Uruguay

International Fellow https://www.sanger.ac.uk/people/faculty/international-fellows/wellcome-international-fellow-dr-gregorio-iraola Wellcome Sanger Institute CB10 1SA, Hinxton, United Kingdom

Adjunct International Professor Center for Integrative Biology https://cib.umayor.cl/en/investigator Universidad Mayor Santiago de Chile, Chile

[csoneson]

@iferres - would you be interested in reviewing this submission for JOSS (see here for more information about our reviewing model)?

[karinlag]

I have to decline, but may I suggest @evezeyl?

[csoneson]

@evezeyl - would you be interested in reviewing this submission for JOSS (see here for more information about our reviewing model)?

[iferres]

Hi, thanks for your consideration. Yes, I will gladly review it.

[csoneson]

@iferres Thank you! Once we have secured one more reviewer I will open the review issue here on GitHub, where you will find more information and be able to generate your review checklist.

[asafpr]

Sorry, I was away. I'll be happy to review it @csoneson

[evezeyl]

Sorry for the late answer. Thank you so much for considering me, but I would have had to decline, i do not currently have the capacity. All the best. Eve

[csoneson]

Thanks @asafpr! I'll assign you and start the review issue. @evezeyl - no problem at all, thanks a lot for letting us know 🙂

[csoneson]

@editorialbot add @iferres as reviewer

[editorialbot]

@iferres added to the reviewers list!

[csoneson]

@editorialbot add @asafpr as reviewer

[editorialbot]

@asafpr added to the reviewers list!

[csoneson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4910.