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

[editorialbot]

Submitting author: @milnus (Magnus Jespersen)
Repository: https://github.com/milnus/Corekaburra
Branch with paper.md (empty if default branch): main
Version: v0.0.5
Editor: @csoneson
Reviewers: @iferres, @asafpr
Archive: 10.5281/zenodo.7344004

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

@iferres & @asafpr, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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

📝 Checklist for @iferres

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (158.1 files/s, 43501.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
SUM:                            24           1042            808           4753
-------------------------------------------------------------------------------


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
- 10.1186/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

[editorialbot]

Wordcount for paper.md is 539

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[csoneson]

👋🏼 @milnus, @iferres, @asafpr - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

[asafpr]

Review checklist for @asafpr

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/milnus/Corekaburra?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@milnus) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[asafpr]

@milnus the workflow wiki page has a broken link to gff files dir, should be https://github.com/asafpr/Corekaburra/tree/main/Example_workflow/Input_Gff_files

[asafpr]

@milnus after panaroo-generate-gffs why should the file names be changed? Is there another use for that script with the original output file names? why not producing the correct file names in this script?

[asafpr]

@milnus the file coreless_contig_accessory_gene_content.tsv is missing from output dir. Also the file core_gene_graph.gml has a typo in the wiki page (core_gene_grapgh.gml) and the last paragraph has some mixed singular/plural. In addition some of the output files are tsv while others are csv, I think they should all be the same. I didn't understand the definition of sub-segments, maybe you can explain it in more detail.
The downstream analysis in my opinion should be wrapped in scripts, at least the most common questions, it will be more user-friendly this way and I think this is the main use-case of the tool.

[asafpr]

@milnus in the paper line 24 "dispite" -> "despite"

[iferres]

Review checklist for @iferres

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/milnus/Corekaburra?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@milnus) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[milnus]

@asafpr - Response to comments:

---

@milnus the workflow wiki page has a broken link to gff files dir, should be

Thanks! Very thorough reading and checking of links. The dead link has now been fixed.

---

@milnus after panaroo-generate-gffs why should the file names be changed? Is there another use for that script with the original output file names? why not producing the correct file names in this script?

The panaroo-generate-gffs script is not part of Corekaburra, but Panaroo. The file names are changed so that Corekaburra can connect the Gff file name to a column in the gene_presence_absence.csv file. The Gff files produced from the panaroo-generate-gffs are very unlikely to be used for any post-processing in Panaroo, as the pan-genome graph is preferred.

---

the file coreless_contig_accessory_gene_content.tsv is missing from output dir

This file is only produced when there are at least one contig with no core genes. This has been clarified in the documentation.

---

Also the file core_gene_graph.gml has a typo in the wiki page (core_gene_grapgh.gml) and the last paragraph has some mixed singular/plural

This has been corrected

---

In addition some of the output files are tsv while others are csv, I think they should all be the same.

Agreed, it was a bit silly. Now everything is converted to .tsv output.

---

I didn't understand the definition of sub-segments, maybe you can explain it in more detail.

The paragraphs core_segments.tsv and no_accessory_core_segments.tsv have both been reworded to hopefully give a cleaner explanation around segments and sub-segments.

---

The downstream analysis in my opinion should be wrapped in scripts, at least the most common questions, it will be more user-friendly this way and I think this is the main use-case of the tool.

I see the point, and it has been debated heavily in our group. We have produced some 'beta' scripts to do small tasks but always find it to be less flexible than using command-line tools to query output files.
Currently our view is that the amount of time for implementation and maintenance is better spend on future feature implementations, likely to detect rearrangements. If we find a query that is not easily made with command-line tools, we will definitely look to make a script.

---

@milnus in the paper line 24 "dispite" -> "despite"

This has been corrected.

[iferres]

Hi @csoneson , all looks ok to me.

[csoneson]

Thanks @iferres!

[asafpr]

I think all the issues I raised were also covered so you've got my ok too.

[csoneson]

That's great, thanks a lot @asafpr!

@milnus - I will also have a look through the submission and get back to you shortly with the next steps.

[csoneson]

@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

[csoneson]

@editorialbot generate pdf

[csoneson]

@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

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[csoneson]

@editorialbot set 0.0.5 as version

[editorialbot]

Done! version is now 0.0.5

[csoneson]

@editorialbot set 10.5281/zenodo.7344004 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7344004

[csoneson]

@milnus Great, thanks! All looks good to me, I will hand over to the track EiC for the final steps. Thanks for submitting to JOSS!

[csoneson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[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

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3742, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot set v0.0.5 as version

[editorialbot]

Done! version is now v0.0.5

[Kevin-Mattheus-Moerman]

@milnus as the AEiC of this track I am here to help process this submission for acceptance. I have just inspected the repository, the archive, this review, and reviewed the paper and all seems in order. I will now proceed to accept this submission.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[Kevin-Mattheus-Moerman]

@milnus Congratulations on this publiction in JOSS!

@csoneson thanks for editing this submission!

Special thanks also to @iferres and @asafpr for their review efforts!!!!!

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04910 joss-papers#3766
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04910
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[editorialbot]

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