[PRE REVIEW]: FASTQE: sequence quality visualisation with Emoji

[editorialbot]

Submitting author: !--author-handle-->@LonsBio<!--end-author-handle-- (Andrew Lonsdale) Repository: https://github.com/fastqe/fastqe Branch with paper.md (empty if default branch): joss Version: v0.3.3 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (716.5 files/s, 121096.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           4            190            262            630
Markdown                         3            128              0            371
TeX                              1             18              0            163
HTML                             1             40              2            125
YAML                             3             12             10             77
-------------------------------------------------------------------------------
SUM:                            12            388            274           1366
-------------------------------------------------------------------------------

Commit count by author:

    59  lonsbio
    31  Andrew Lonsdale
     4  Phil Ewels
     2  Clare Sloggett
     1  Frédéric Mahé
     1  Helena Rasche
     1  cjwomack

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1365

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1093/nar/gkp1137 is OK
- 10.1073/pnas.85.8.2444 is OK
- 10.1093/bioinformatics/btp163 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: FastQC
- No DOI given, and none found for title: Quality Control (Galaxy Training Materials)

❌ MISSING DOIs

- 10.1093/bioinformatics/btu170 may be a valid DOI for title: Trimmomatic: a flexible trimmer for Illumina seque...
- 10.12688/f1000research.21142.2 may be a valid DOI for title: Falco: high-speed FastQC emulation for quality con...
- 10.1093/bioinformatics/bty560 may be a valid DOI for title: fastp: an ultra-fast all-in-one FASTQ preprocessor
- 10.24918/cs.2021.17 may be a valid DOI for title: A fun introductory command line lesson: Next gener...

❌ INVALID DOIs

- None

[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:

fqfa: A pure Python package for genomic sequence files Submitting author: @afrubin Handling editor: @lpantano (Active) Reviewers: @natir, @FlorianThibord Similarity score: 0.6388

Nextclade: clade assignment, mutation calling and quality control for viral genomes Submitting author: @rneher Handling editor: @kellyrowland (Active) Reviewers: @kevinlibuit, @DavidNickle Similarity score: 0.6363

Nanoq: ultra-fast quality control for nanopore reads Submitting author: @esteinig Handling editor: @luizirber (Active) Reviewers: @natir, @bovee Similarity score: 0.6363

pycoQC, interactive quality control for Oxford Nanopore Sequencing Submitting author: @a-slide Handling editor: @pjotrp (Retired) Reviewers: @george-githinji Similarity score: 0.6353

CutePeaks: A modern viewer for Sanger trace file Submitting author: @dridk Handling editor: @lpantano (Active) Reviewers: @tobiasrausch, @wdecoster Similarity score: 0.6313

⚠️ 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]

@lonsbio thanks for this submission. Although this work looks well done and maybe useful for some for quick visual inspection of data, we would not classify this as scientific research software (e.g. of such importance that it directly influences scientific findings and that one would feel the need to cite it in subsequent research work). Hence this work is unfortunately not in scope for JOSS.

We will now proceed to reject this submission.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.