[REVIEW]: Nextclade: clade assignment, mutation calling and quality control for viral genomes

[whedon]

Submitting author: @rneher (Richard Neher)
Repository: https://github.com/nextstrain/nextclade
Version: v1.4.5
Editor: @kellyrowland
Reviewers: @kevinlibuit, @DavidNickle
Archive: 10.5281/zenodo.5726681

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b0e8e7f231ddfc61616de6b56f32b79f/status.svg)](https://joss.theoj.org/papers/b0e8e7f231ddfc61616de6b56f32b79f)

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

@kevinlibuit & @DavidNickle, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kellyrowland 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 ✨

Review checklist for @kevinlibuit

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@rneher) 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

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.) #3862

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 and who the target audience is?
• 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?

Review checklist for @DavidNickle

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@rneher) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @kevinlibuit, @DavidNickle it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1366

[whedon]

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

OK DOIs

- 10.1016/0022-2836(81)90087-5 is OK
- 10.21105/joss.02906 is OK
- 10.1093/bioinformatics/bty407 is OK
- 10.1038/s41588-021-00862-7 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/molbev/mst010 is OK
- 10.1038/s41564-021-00932-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.56 s (581.6 files/s, 155780.7 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
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C/C++ Header                           505          26178          30150         110385
TypeScript                             348           3184            514          16565
Markdown                               145           4668              0          13575
Python                                  33           1984           3786           7857
CMake                                  120           1064           1230           5043
SVG                                     13              3              3           2076
Bourne Shell                            31            471            325           2008
YAML                                    40            255            134           1823
C                                        4            160            100           1300
Windows Module Definition               16            166            109           1114
make                                     9            193            143            800
Sass                                    13            165             19            757
JavaScript                              22            104             77            694
diff                                    17            121            437            398
XML                                      7              7             10            387
Dockerfile                               4             50             11            195
Bourne Again Shell                       1             20              8            165
Objective-C                              3             61             41            150
SWIG                                     1             21              3            142
Windows Resource File                    3             68             89            139
reStructuredText                         5            133            140            124
TeX                                      1             11              0            121
DOS Batch                                4             26             46             83
CSS                                      3             14              3             60
Bazel                                    2              5              0             44
PowerShell                               1             12              0             23
Meson                                    1              4              0             19
HTML                                     2              2              0             18
---------------------------------------------------------------------------------------
SUM:                                  2070          62960          56568         434879
---------------------------------------------------------------------------------------


Statistical information for the repository '03769d07d8138fa5c149f54c' was
gathered on 2021/09/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Cornelius Roemer                 6           108              3            0.03
Richard Neher                   32           800            266            0.24
eharkins                         1             1              2            0.00
ivan-aksamentov                450        391278          42795           99.73

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Richard Neher                63            7.9         11.1                7.94
eharkins                      1          100.0          1.2                0.00
ivan-aksamentov          349902           89.4          4.2               17.14

[DavidNickle]

Conflict of interest: I confirm that I have read the JOSS conflict of interest 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

Repository: The source code for this software is available at the repository url
clicking through the link Nextclade CLI
https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli.html

License: The repository contains a plain-text LICENSE file with the contents of an OSI approved software license.
All source code is freely available under the terms of the GNU Affero General Public License.

Contribution and authorship: It is not clear who did what for the paper

Functionality: The software is functional and important adding very important knowledge to the public domain - I particular like the alignment algorithm takes information about different readings.

Installation: The installation procedure follows the documentation clearly - I followed the Nextclade CLI method and ran it the SARS-CoV-2 example. From:
./nextclade dataset get --name='sars-cov-2' --output-dir='data/sars-cov-2'

Functionality: I confirmed the functional claims of the on the tutorial data as well as some of my own.

Performance: It appears to quick! But the authors did not claim anything around speed.

A statement of need: The authors have a clear audience in mine and the paper and the software should be readably available to that audience.

Installation instructions: Following the command line instructions for Nextclade CLI works as claimed. I fallowed the Mac instructions.

Example usage: I went through the the SARS-CoV-2 example and all the functionality worked. I found exercise easy and straight forward.
$ ./nextclade run --input-dataset=data/sars-cov-2/ --input-fasta=data/sars-cov-2/sequences.fasta

Automated tests: YES — tests are available
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. YES - but they should start with Nextstrain base install. This is declared in the Nextclade CLI install page.

Software paper: YES

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided? YES

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is? YES

State of the field: Do the authors describe how this software compares to other commonly-used packages? YES
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)? YES
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? YES

Lastly, the banded pairwise Smith-Waterman alignment is a nice idea and I can imaging implementing that method in mofft or another multiple sequence aligner.

This should be accepted as is.

[EduanWilkinson]

@whedon I accept to review the manuscript. Please add me as a reviewer.

Eduan

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[EduanWilkinson]

@kellyrowland Please advise if you still need me to review.

Eduan

[kellyrowland]

@whedon add @EduanWilkinson as reviewer

[whedon]

OK, @EduanWilkinson is now a reviewer

[kellyrowland]

Hi @EduanWilkinson - thanks for your interest! I've added you as a reviewer here; you've been assigned to the Github issue. I will edit the top post to create a set of checkboxes for you to work through for the paper review.

Please feel free to @ me here if you have any questions or run into any issues (I am on vacation this next week though, so my response will be delayed).

[kevinlibuit]

Hey, @kellyrowland <https://github.com/kellyrowland>! Was I unassigned as a reviewer? Apologies for not keeping up with the thread; I saw that I had six weeks to complete the review so have put this away for a bit. Though I just tried to start the process today and am now seeing that I've been unassigned. Please let me know if you need my assistance for review. Best, Kevin

…

On Fri, Oct 1, 2021 at 4:01 PM Kelly L. Rowland ***@***.***> wrote: Hi @EduanWilkinson <https://github.com/EduanWilkinson> - thanks for your interest! I've added you as a reviewer here; you've been assigned to the Github issue. I will edit the top post to create a set of checkboxes for you to work through for the paper review. Please feel free to @ me here if you have any questions or run into any issues (I am on vacation this next week though, so my response will be delayed). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3773 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE2GNXLEXFGOO44VIKTDLLDUEY4S5ANCNFSM5E4O5ZDQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[kevinlibuit]

Whoops. My mistake. I'm a JOSS reviewer NOOB. I guess I was unassigned on the pre-review issue that has since been closed. I think I'm following things now, though I am unable to update the checklist and cannot access the invitation link:

Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

[kellyrowland]

Hi @kevinlibuit - it looks like you were successfully assigned to this review issue, so please proceed with your review at your earliest convenience. I was out of office last week but am back online; feel free to @ me with any questions or concerns.

[whedon]

👋 @DavidNickle, please update us on how your review is going (this is an automated reminder).

[rneher]

@kellyrowland sorry for bugging, but somehow this process seems stalled. kevinlibuit has finished his review, as did DavidNickle (but the check-boxes are not ticked). And we haven't heard from EduanWilkinson in a while.

[kellyrowland]

Thanks for the ping on this, @rneher . Since we have two reviewers who have recommended the submission for acceptance, I'll proceed with the checkout process.

(That is, I will check off the review boxes for DavidNickle and remove EduanWilkinson as a reviewer.)

Could you please create a new tagged software release (if the software has changed in this review process) and archive the release (on Zenodo, figshare, etc.) and then post the version number and archive DOI here in this review issue?

[kellyrowland]

I have updated the top post in this issue as per my above note.

@EduanWilkinson thank you for your interest here - we're going to proceed with the paper acceptance since we have positive recommendations from two reviewers at this point. I do hope that you'll consider reviewing for JOSS in the future.

[rneher]

thanks, @kellyrowland. Will post version and DOI soon!

[rneher]

Hi @kellyrowland
I made a DOI for version 1.4.5 at Zenodo:

Version 1.4.5
10.5281/zenodo.5726681

https://zenodo.org/record/5726681

We'll have automated registration with zenodo for future releases, but weren't quite ready to make a new release just now.

[kellyrowland]

@whedon set 10.5281/zenodo.5726681 as archive

[whedon]

OK. 10.5281/zenodo.5726681 is the archive.

[kellyrowland]

@whedon set v1.4.5 as version

[whedon]

OK. v1.4.5 is the version.

[kellyrowland]

@whedon generate pdf

[whedon]

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

[kellyrowland]

@whedon check references

[whedon]

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

OK DOIs

- 10.1016/0022-2836(81)90087-5 is OK
- 10.21105/joss.02906 is OK
- 10.1093/bioinformatics/bty407 is OK
- 10.1038/s41588-021-00862-7 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/molbev/mst010 is OK
- 10.1038/s41564-021-00932-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kellyrowland]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/0022-2836(81)90087-5 is OK
- 10.21105/joss.02906 is OK
- 10.1093/bioinformatics/bty407 is OK
- 10.1038/s41588-021-00862-7 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/molbev/mst010 is OK
- 10.1038/s41564-021-00932-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2774

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2774, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@kellyrowland and @rneher - thanks for passing this on in such good condition. Looks ready to go!

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03773 joss-papers#2779
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03773
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...

[kthyng]

Congrats on your new publication @rneher! Many thanks to editor @kellyrowland and reviewers @kevinlibuit and @DavidNickle for your time, hard work, and expertise!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03773/status.svg)](https://doi.org/10.21105/joss.03773)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03773">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03773/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03773/status.svg
   :target: https://doi.org/10.21105/joss.03773

This is how it will look in your documentation:

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