[PRE REVIEW]: Back to sequences: find the origin of k-mers #6872

editorialbot · 2024-06-11T07:42:55Z

Submitting author: @pierrepeterlongo (Pierre Peterlongo)
Repository: https://github.com/pierrepeterlongo/back_to_sequences/
Branch with paper.md (empty if default branch):
Version: v0.6.5
Editor: @majensen
Reviewers: @Anjan-Purkayastha, @amoeba
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21/status.svg)](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-06-11T07:42:57Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2024-06-11T07:43:31Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1098.6 files/s, 187191.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                            11            357            216           1792
CSV                              3              0              0           1497
Markdown                         4            112              0            543
TeX                              1             26              3            200
Python                           6             50             37            152
Bourne Shell                     4             38             23            144
TOML                             1             12              5             38
YAML                             1             11              0             26
-------------------------------------------------------------------------------
SUM:                            31            606            284           4392
-------------------------------------------------------------------------------

Commit count by author:

   122	Pierre Peterlongo
    13	Pierre Marijon
    10	Anthony Baire
     7	PETERLONGO Pierre
     1	Francesco Andreace

editorialbot · 2024-06-11T07:43:35Z

Paper file info:

📄 Wordcount for paper.md is 2346

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-06-11T07:43:37Z

License info:

🔴 Failed to discover a valid open source license

editorialbot · 2024-06-11T07:43:41Z

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

OK DOIs

- 10.1038/s41579-020-0364-5 is OK

MISSING DOIs

- No DOI given, and none found for title: The Platinum Searcher
- No DOI given, and none found for title: The Silver Searcher
- No DOI given, and none found for title: Kmer Mapper
- 10.1101/2021.12.03.471074 may be a valid DOI for title: KAGE: Fast alignment-free graph-based genotyping o...
- 10.1038/nmeth.1376 may be a valid DOI for title: Sense from sequence reads: methods for alignment a...
- 10.1101/gr.101360.109 may be a valid DOI for title: Assembly of large genomes using second-generation ...
- No DOI given, and none found for title: Multiple comparative metagenomics using multiset k...
- 10.1093/bfgp/elr035 may be a valid DOI for title: Comparison of the two major classes of assembly al...
- No DOI given, and none found for title: Skmer: assembly-free and alignment-free sample ide...
- 10.1093/bioinformatics/btu288 may be a valid DOI for title: RNA-Skim: a rapid method for RNA-Seq quantificatio...
- 10.1093/nar/gku1187 may be a valid DOI for title: Reference-free detection of isolated SNPs
- 10.1093/bioadv/vbac029 may be a valid DOI for title: Kmtricks: efficient and flexible construction of b...
- 10.1101/gr.277615.122 may be a valid DOI for title: Extremely fast construction and querying of compac...
- 10.1145/585265.585267 may be a valid DOI for title: The greedy path-merging algorithm for contig scaff...
- 10.1089/cmb.2012.0021 may be a valid DOI for title: SPAdes: a new genome assembly algorithm and its ap...
- 10.1016/j.dam.2018.03.035 may be a valid DOI for title: A resource-frugal probabilistic dictionary and app...
- 10.1186/s13059-019-1891-0 may be a valid DOI for title: Improved metagenomic analysis with Kraken 2
- No DOI given, and none found for title: k mdiff, large-scale and user-friendly differentia...
- 10.1186/s12864-015-1406-7 may be a valid DOI for title: Quality control of microbiota metagenomics by k-me...
- 10.1016/j.isci.2023.108057 may be a valid DOI for title: aKmerBroom: Ancient oral DNA decontamination using...
- No DOI given, and none found for title: {AH}ash: A Load-Balanced One Permutation Hash

INVALID DOIs

- None

editorialbot · 2024-06-11T07:44:12Z

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

editorialbot · 2024-06-11T15:31:20Z

Hello @pierrepeterlongo, here are the things you can ask me to do:


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pierrepeterlongo · 2024-06-11T15:34:43Z

@editorialbot commands

editorialbot · 2024-06-11T15:34:47Z

Hello @pierrepeterlongo, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
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# Get a link to the complete list of reviewers
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editorialbot · 2024-06-11T15:49:08Z

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@article{flicek2009sensetitle={Sense from sequence reads: methods for alignment and assembly},author={Flicek, Paul and Birney, Ewan},journal={Nature methods},volume={6},number={Suppl 11},pages={S6--S12},year={2009},doi=‘

pierrepeterlongo · 2024-06-11T15:50:08Z

@editorialbot check references

editorialbot · 2024-06-11T15:50:25Z

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

OK DOIs

- 10.1186/s13059-022-02771-2 is OK
- 10.1038/nmeth.1376 is OK
- 10.1101/gr.101360.109 is OK
- 10.7717/peerj-cs.94 is OK
- 10.1093/bfgp/elr035 is OK
- 10.1093/bioinformatics/btu288 is OK
- 10.1093/nar/gku1187 is OK
- 10.1093/bioadv/vbac029 is OK
- 10.1101/gr.277615.122 is OK
- 10.1145/585265.585267 is OK
- 10.1089/cmb.2012.0021 is OK
- 10.1016/j.dam.2018.03.035 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/s41579-020-0364-5 is OK
- 10.1093/bioinformatics/btac689 is OK
- 10.1186/s12864-015-1406-7 is OK
- 10.1016/j.isci.2023.108057 is OK

MISSING DOIs

- No DOI given, and none found for title: The Platinum Searcher
- No DOI given, and none found for title: The Silver Searcher
- No DOI given, and none found for title: Kmer Mapper
- No DOI given, and none found for title: AHash: A Load-Balanced One Permutation Hash

INVALID DOIs

- 10.1186/s13059 is INVALID

pierrepeterlongo · 2024-06-11T15:57:26Z

@pierrepeterlongo 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.

We may suggest
Brice Letcher
Anuradha Wickramarachchi
Michael B. Hall

pierrepeterlongo · 2024-06-11T20:41:33Z

@editorialbot list reviewers

editorialbot · 2024-06-11T20:41:35Z

Please log in the JOSS Reviewers site to search through the list of current reviewers.

pierrepeterlongo · 2024-06-17T09:56:35Z

@editorialbot check repository

editorialbot · 2024-06-17T09:56:57Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1373.1 files/s, 234673.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                            11            357            216           1792
CSV                              3              0              0           1497
Markdown                         4            112              0            543
TeX                              1             26              3            216
Python                           6             50             37            152
Bourne Shell                     4             38             23            144
TOML                             1             12              5             38
YAML                             1             11              0             26
-------------------------------------------------------------------------------
SUM:                            31            606            284           4408
-------------------------------------------------------------------------------

Commit count by author:

   127	Pierre Peterlongo
    13	Pierre Marijon
    10	Anthony Baire
     7	PETERLONGO Pierre
     1	Francesco Andreace

editorialbot · 2024-06-17T09:57:09Z

Paper file info:

📄 Wordcount for paper.md is 2348

✅ The paper includes a Statement of need section

editorialbot · 2024-06-17T09:57:11Z

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

pierrepeterlongo · 2024-06-19T09:07:47Z

Submitting author: @pierrepeterlongo (Pierre Peterlongo) Repository: https://github.com/pierrepeterlongo/back_to_sequences/ Branch with paper.md (empty if default branch): Version: v0.6.5 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

Status badge code:
HTML: <a href="https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21"><img src="https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21/status.svg)](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21)
Author instructions

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

@pierrepeterlongo 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:
@editorialbot commands

Suggested reviewers:
Brice Letcher
Anuradha Wickramarachchi
Michael B. Hall

Kevin-Mattheus-Moerman · 2024-06-24T14:38:31Z

@editorialbot generate pdf

editorialbot · 2024-06-24T14:39:49Z

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

editorialbot · 2024-06-24T14:40:33Z

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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.

Kevin-Mattheus-Moerman · 2024-07-03T10:04:09Z

@pierrepeterlongo thanks for making those updates/changes to have your paper conform more to our standards. As AEiC for this track I am currently pre-reviewing your submission and am also looking for a handling editor. Since all editors in this domain are pre-occupied with other submissions it may take a longer than usual to find/assign an editor. Hence I've just added the waitlisted label. We'll assign an editor as soon as one becomes available.

For the moment could you work on the below points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
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/).
I have only had a quick look at your submission so far, but the README does not seem to link to: 1) automated testing, and 2) dedicated project documentation. Please add these and link to them clearly in the README.

pierrepeterlongo · 2024-07-03T10:31:07Z

@editorialbot check references

editorialbot · 2024-07-03T10:31:28Z

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

OK DOIs

- 10.1186/s13059-022-02771-2 is OK
- 10.1038/nmeth.1376 is OK
- 10.1101/gr.101360.109 is OK
- 10.7717/peerj-cs.94 is OK
- 10.1093/bfgp/elr035 is OK
- 10.1186/s13059-019-1632-4 is OK
- 10.1093/bioinformatics/btu288 is OK
- 10.1093/nar/gku1187 is OK
- 10.1093/bioadv/vbac029 is OK
- 10.1101/gr.277615.122 is OK
- 10.1145/585265.585267 is OK
- 10.1089/cmb.2012.0021 is OK
- 10.1016/j.dam.2018.03.035 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/s41579-020-0364-5 is OK
- 10.1093/bioinformatics/btac689 is OK
- 10.1186/s12864-015-1406-7 is OK
- 10.1016/j.isci.2023.108057 is OK

MISSING DOIs

- No DOI given, and none found for title: The Platinum Searcher
- No DOI given, and none found for title: The Silver Searcher
- No DOI given, and none found for title: Kmer Mapper
- No DOI given, and none found for title: AHash: A Load-Balanced One Permutation Hash

INVALID DOIs

- None

pierrepeterlongo · 2024-07-03T12:36:06Z

Thanks @Kevin-Mattheus-Moerman for your feedbacks.

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

The last entries with no DOI are citations of github repositories. Maybe this is not the right way to do?

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/).

We have added a contributing.md file indicating contributing guidelines.

I have only had a quick look at your submission so far, but the README does not seem to link to: 1) automated testing, and 2) dedicated project documentation. Please add these and link to them clearly in the README.

The documentation is now in a separate readthedocs repository: https://b2s-doc.readthedocs.io/en
We will inform you when the link to automated testing is ready

Thanks,
Pierre

pierrepeterlongo · 2024-07-14T08:53:42Z

Hello there,

Links to automated testing are now ready and linked in the readme.
All points you mentioned are now fixed.

Pierre

Kevin-Mattheus-Moerman · 2024-07-30T07:34:04Z

@editorialbot invite @majensen as editor

editorialbot · 2024-07-30T07:34:06Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2024-07-30T07:36:41Z

@pierrepeterlongo I've invited an editor who I hope can handle this submission. I have looked at the automated testing link. Are you referring to the testing badge? That link does not seem to work. Could you also link to the contributing.md file from the readme?

majensen · 2024-07-30T13:48:47Z

@editorialbot assign me as editor

editorialbot · 2024-07-30T13:48:51Z

Assigned! @majensen is now the editor

majensen · 2024-07-31T01:52:10Z

Hi @amoeba - could I get your help on this work for JOSS? I think it's right up your alley. --@majensen

majensen · 2024-07-31T02:05:18Z

Checking with another potential reviewer offline.

majensen · 2024-08-01T00:54:16Z

Thanks so much @Anjan-Purkayastha for agreeing to review this work. I will add you to the reviewers now; the review will start after I find one more reviewer and open the official review issue.

majensen · 2024-08-01T00:54:39Z

@editorialbot add @Anjan-Purkayastha as reviewer

editorialbot · 2024-08-01T00:54:41Z

@Anjan-Purkayastha added to the reviewers list!

amoeba · 2024-08-01T16:50:02Z

Hi @majensen, I can review this one.

majensen · 2024-08-01T19:27:22Z

@amoeba very much appreciated

majensen · 2024-08-01T19:27:41Z

@editorialbot add @amoeba as reviewer

editorialbot · 2024-08-01T19:27:44Z

@amoeba added to the reviewers list!

majensen · 2024-08-01T19:28:10Z

@editorialbot start review

editorialbot · 2024-08-01T19:28:14Z

OK, I've started the review over in #7066.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 11, 2024

editorialbot added Rust Shell Python labels Jun 11, 2024

editorialbot added the TeX label Jun 17, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jul 3, 2024

editorialbot assigned majensen Jul 30, 2024

majensen removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jul 31, 2024

editorialbot assigned amoeba Aug 1, 2024

editorialbot closed this as completed Aug 1, 2024

This was referenced Aug 27, 2024

Suggestions on improving your manuscript and documentation. pierrepeterlongo/back_to_sequences#6

Closed

JOSS Review pierrepeterlongo/back_to_sequences#8

Closed

[PRE REVIEW]: Back to sequences: find the origin of k-mers #6872

[PRE REVIEW]: Back to sequences: find the origin of k-mers #6872

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