[PRE REVIEW]: Mashpit: sketching out genomic epidemiology

[editorialbot]

Submitting author: !--author-handle-->@tongzhouxu<!--end-author-handle-- (Tongzhou Xu) Repository: https://github.com/tongzhouxu/mashpit Branch with paper.md (empty if default branch): Version: v0.9.7 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @hkaspersen, @mberacochea Managing EiC: Kevin M. Moerman

Status

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Author instructions

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

@tongzhouxu if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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

✅ OK DOIs

- 10.21105/joss.00027 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Mash: fast genome and metagenome distance estimati...
- No DOI given, and none found for title: BLAST+: architecture and applications
- No DOI given, and none found for title: SeqSero2: rapid and improved Salmonella serotype d...
- No DOI given, and none found for title: The EnteroBase user’s guide, with case studies on ...

❌ MISSING DOIs

- 10.1093/bioinformatics/bty407 may be a valid DOI for title: Nextstrain: real-time tracking of pathogen evoluti...
- 10.2807/1560-7917.es.2017.22.23.30544 may be a valid DOI for title: PulseNet International: Vision for the implementat...
- 10.3389/fmicb.2017.00375 may be a valid DOI for title: A comparative analysis of the Lyve-SET phylogenomi...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1021.4 files/s, 91690.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            138            158           1050
Markdown                         2             45              0            192
HTML                             4             11              2            155
YAML                             4             11             11             97
TeX                              1              9              0             81
JavaScript                       2              0              7              2
CSS                              1              0              5              1
-------------------------------------------------------------------------------
SUM:                            22            214            183           1578
-------------------------------------------------------------------------------

Commit count by author:

   146  Tongzhou Xu
    14  tongzhouxu
     7  dependabot[bot]
     3  Lee Katz
     1  Lee Katz - Aspen
     1  Lee Katz gzu2

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1217

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

Sepia, a taxonomy oriented read classifier in Rust Submitting author: @hcdenbakker Handling editor: @will-rowe (Retired) Reviewers: @Ebedthan, @telatin Similarity score: 0.7201

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis Submitting author: @hkaspersen Handling editor: @csoneson (Active) Reviewers: @mberacochea, @hseabolt, @rcannood Similarity score: 0.7082

NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases Submitting author: @ktmeaton Handling editor: @lpantano (Active) Reviewers: @coughls, @druvus Similarity score: 0.7064

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Submitting author: @lskatz Handling editor: @lpantano (Active) Reviewers: @lfaller, @erinyoung, @druvus Similarity score: 0.7000

Finch: a tool adding dynamic abundance filtering to genomic MinHashing Submitting author: @bovee Handling editor: @biorelated (Retired) Reviewers: @HadrienG Similarity score: 0.6991

⚠️ 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.

[tongzhouxu]

@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:

[editorialbot]

Five most similar historical JOSS papers:

Sepia, a taxonomy oriented read classifier in Rust Submitting author: @hcdenbakker Handling editor: @will-rowe (Retired) Reviewers: @Ebedthan, @telatin Similarity score: 0.7202

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis Submitting author: @hkaspersen Handling editor: @csoneson (Active) Reviewers: @mberacochea, @hseabolt, @rcannood Similarity score: 0.7084

NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases Submitting author: @ktmeaton Handling editor: @lpantano (Active) Reviewers: @coughls, @druvus Similarity score: 0.7065

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Submitting author: @lskatz Handling editor: @lpantano (Active) Reviewers: @lfaller, @erinyoung, @druvus Similarity score: 0.7000

Finch: a tool adding dynamic abundance filtering to genomic MinHashing Submitting author: @bovee Handling editor: @biorelated (Retired) Reviewers: @HadrienG Similarity score: 0.6991

⚠️ 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.

[tongzhouxu]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1093/bioinformatics/bty407 is OK
- 10.2807/1560-7917.es.2017.22.23.30544 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.21105/joss.00027 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1128/aem.01746-19 is OK
- 10.1101/gr.251678.119 is OK
- 10.3389/fmicb.2017.00375 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@tongzhouxu Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• [ ] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• [ ] In the paper, please spell out USA as United States of America.

[Kevin-Mattheus-Moerman]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[tongzhouxu]

@tongzhouxu Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• [ ] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• [ ] In the paper, please spell out USA as United States of America.

Thank you for the suggestions. I have added a CONTRIBUTING.md in the latest commit.

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

👋🏻 @tongzhouxu - thanks for your submission. I will handle it from here, and start by finding two suitable reviewers. If you have any suggestions (e.g. from the list mentioned in the top comment), feel free to let me know.

[csoneson]

👋🏻 @hkaspersen, @mberacochea, @ns-rse - would you be interested in reviewing this submission for JOSS?

Mashpit: sketching out genomic epidemiology https://github.com/openjournals/joss-reviews/issues/7235

Thanks in advance!

[mberacochea]

Hi @csoneson,

I'm happy to review this submission. However, I won't be able to start until next week at the earliest. If that is not a problem, I'm happy to proceed.

Cheers

[hkaspersen]

@csoneson Thank you for the invitation! I would be happy to review this. Where can I find review criteria etc?

[csoneson]

Hi @hkaspersen and @mberacochea - thanks a lot for accepting to review! I will assign you and start the review issue.

@mberacochea - next week is totally fine! @hkaspersen - you can find more information here. I'm starting the review issue now, and in there you will find more practical instructions, including how to create your checklist.

[csoneson]

@editorialbot add @hkaspersen as reviewer

[editorialbot]

@hkaspersen added to the reviewers list!

[csoneson]

@editorialbot add @mberacochea as reviewer

[editorialbot]

@mberacochea 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/7306.