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

Closed editorialbot closed 2 months ago

editorialbot commented 3 months ago

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

Status

status

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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.

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editorialbot commented 3 months ago

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

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 3 months ago

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 commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2346

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 3 months ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 3 months ago 
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 commented 3 months ago

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

editorialbot commented 3 months ago

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
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
pierrepeterlongo commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

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
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
editorialbot commented 3 months ago

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 commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago 
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 commented 3 months ago

@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 commented 3 months ago

@editorialbot list reviewers

editorialbot commented 3 months ago

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

pierrepeterlongo commented 3 months ago

@editorialbot check repository

editorialbot commented 3 months ago

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 commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2348

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

pierrepeterlongo commented 3 months ago

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

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 commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

editorialbot commented 3 months ago

Five most similar historical JOSS papers:

Metagenomic classification with KrakenUniq on low-memory computers Submitting author: @salzberg Handling editor: @lpantano (Active) Reviewers: @Jessime, @MaximLippeveld Similarity score: 0.6703

Sepia, a taxonomy oriented read classifier in Rust Submitting author: @hcdenbakker Handling editor: @will-rowe (Retired) Reviewers: @Ebedthan, @telatin Similarity score: 0.6590

Koverage: Read-coverage analysis for massive (meta)genomics datasets Submitting author: @beardymcjohnface Handling editor: @csoneson (Active) Reviewers: @lparsons, @telatin Similarity score: 0.6562

ReferenceSeeker: rapid determination of appropriate reference genomes Submitting author: @oschwengers Handling editor: @will-rowe (Retired) Reviewers: @standage, @luizirber Similarity score: 0.6558

ROCK: digital normalization of whole genome sequencing data Submitting author: @alex2cris Handling editor: @luizirber (Active) Reviewers: @hiraksarkar, @ctb Similarity score: 0.6555

⚠️ 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 commented 3 months ago

@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:

pierrepeterlongo commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago 
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 commented 3 months ago

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 commented 2 months ago

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 commented 2 months ago

@editorialbot invite @majensen as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 2 months ago

@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 commented 2 months ago

@editorialbot assign me as editor

editorialbot commented 2 months ago

Assigned! @majensen is now the editor

majensen commented 2 months ago

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

majensen commented 2 months ago

Checking with another potential reviewer offline.

majensen commented 2 months ago

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 commented 2 months ago

@editorialbot add @Anjan-Purkayastha as reviewer

editorialbot commented 2 months ago

@Anjan-Purkayastha added to the reviewers list!

amoeba commented 2 months ago

Hi @majensen, I can review this one.

majensen commented 2 months ago

@amoeba very much appreciated

majensen commented 2 months ago

@editorialbot add @amoeba as reviewer

editorialbot commented 2 months ago

@amoeba added to the reviewers list!

majensen commented 2 months ago

@editorialbot start review

editorialbot commented 2 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7066.