[PRE REVIEW]: Prokaryome: A Comprehensive WDL-Based Workflow for Prokaryotic Genome Assembly, Polishing, Annotation, and Visualization

[editorialbot]

Submitting author: @saifeldeen-bio (Saifeldeen M. Ibrahim)
Repository: https://github.com/saifeldeen-bio/Prokaryome
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (881.4 files/s, 58064.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             64              0            228
TeX                              1              1              0            175
YAML                             1              1              4             26
JSON                             1              0              0             14
Python                           1              0              0             11
Bourne Shell                     2              0              0              3
-------------------------------------------------------------------------------
SUM:                             8             66              4            457
-------------------------------------------------------------------------------

Commit count by author:

    44	Saifeldeen Mohamed

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 601

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Genomics in the cloud: using Docker, GATK, and WDL...
- No DOI given, and none found for title: QUAST: quality assessment tool for genome assembli...
- No DOI given, and none found for title: Automated assembly scaffolding using RagTag elevat...

❌ MISSING DOIs

- 10.1007/s13205-024-04065-9 may be a valid DOI for title: Exploring microbial diversity in the rhizosphere: ...
- 10.1371/journal.pone.0030619 may be a valid DOI for title: NGS QC Toolkit: a toolkit for quality control of n...
- 10.11620/ijob.2021.46.3.146 may be a valid DOI for title: Trimming conditions for DADA2 analysis in QIIME2 p...
- 10.1016/j.ygeno.2011.05.009 may be a valid DOI for title: Btrim: a fast, lightweight adapter and quality tri...
- 10.3389/fgene.2014.00013 may be a valid DOI for title: On the optimal trimming of high-throughput mRNA se...
- 10.1371/journal.pcbi.1005595 may be a valid DOI for title: Unicycler: resolving bacterial genome assemblies f...
- 10.1371/journal.pcbi.1007981 may be a valid DOI for title: The genome polishing tool POLCA makes fast and acc...
- 10.1093/bioinformatics/btw354 may be a valid DOI for title: MultiQC: summarize analysis results for multiple t...
- 10.1093/bioinformatics/btu170 may be a valid DOI for title: Trimmomatic: a flexible trimmer for Illumina seque...
- 10.1089/cmb.2012.0021 may be a valid DOI for title: SPAdes: a new genome assembly algorithm and its ap...
- 10.1093/bioinformatics/btac137 may be a valid DOI for title: BWA-MEME: BWA-MEM emulated with a machine learning...
- 10.1093/gigascience/giab008 may be a valid DOI for title: Twelve years of SAMtools and BCFtools
- 10.1371/journal.pone.0112963 may be a valid DOI for title: Pilon: an integrated tool for comprehensive microb...
- 10.1093/bioinformatics/btu153 may be a valid DOI for title: Prokka: rapid prokaryotic genome annotation
- 10.1371/journal.pcbi.1010998 may be a valid DOI for title: GenoVi, an open-source automated circular genome v...

❌ INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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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.

[saifeldeen-bio]

I'd like to suggest the following names to review the paper

1. Devang Thakkar
2. Juke34
3. snamburi3
   thank you so much for your kind consideration.

[Kevin-Mattheus-Moerman]

@saifeldeen-bio 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:

• 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/).

Note also that we are currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy. Hence we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[saifeldeen-bio]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "doi" (NAME) ["@", #<BibTeX::Entry >, {:title=>["Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications"], :author=>["Rajguru, Bhumi and Shri, Manju and Bhatt, Vaibhav D"], :journal=>["3 Biotech"], :volume=>["14"], :number=>["10"], :pages=>["224"], :year=>["2024"], :publisher=>["Springer"]}]

[saifeldeen-bio]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/s13205-024-04065-9 is OK
- 10.1371/journal.pone.0030619 is OK
- 10.11620/IJOB.2021.46.3.146 is OK
- 10.1016/j.ygeno.2011.05.009 is OK
- 10.3389/fgene.2014.00013 is OK
- 10.1371/journal.pcbi.1005595 is OK
- 10.1371/journal.pcbi.1007981 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1093/bioinformatics/btu170 is OK
- 10.1089/cmb.2012.0021 is OK
- 10.1093/bioinformatics/btac137 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1371/journal.pone.0112963 is OK
- 10.1093/bioinformatics/btt086 is OK
- 10.1186/s13059-022-02823-7 is OK
- 10.1093/bioinformatics/btu153 is OK
- 10.1371/journal.pcbi.1010998 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Genomics in the cloud: using Docker, GATK, and WDL...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[saifeldeen-bio]

@editorialbot commands

[editorialbot]

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# List all available commands
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[saifeldeen-bio]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
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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.

[saifeldeen-bio]

@Kevin-Mattheus-Moerman Thank you so much for your kind assistance. I've added the DOIs in the appropriate format. Additionally, I've added the CONTRIBUTING.md inside the paper directory. the CODE_OF_CONDUCT.md is placed in the blob directory