[PRE REVIEW]: Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker

[editorialbot]

Submitting author: @SarahMaman (MAMAN Sarah)
Repository: https://forgemia.inra.fr/bios4biol/intronseeker
Branch with paper.md (empty if default branch): master
Version: v1.0
Editor: @kellyrowland
Reviewers: @CFGrote, @tkchafin
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78"><img src="https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78/status.svg)](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78)

Author instructions

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

@SarahMaman 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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Software report:

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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1746

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- 10.1186/1471-2105-15-293 is OK
- 10.1038/nsmb.2143 is OK
- 10.1038/s41477-020-0688-1 is OK
- 10.1101/gr.177790.114 is OK

MISSING DOIs

- 10.1093/bioinformatics/btp352 may be a valid DOI for title: The sequence alignment/map format and SAMtools
- 10.1038/nmeth.3317 may be a valid DOI for title: HISAT: a fast spliced aligner with low memory requirements
- 10.1093/nar/gks251 may be a valid DOI for title: Grinder: a versatile amplicon and shotgun sequence simulator
- 10.1038/nmeth.3176 may be a valid DOI for title: Fast and sensitive protein alignment using DIAMOND

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@SarahMaman thanks for this submission. As AEiC for this track I am here to help process initial steps. For the moment, can you please try to address the above potentially missing DOIs? ☝️ You can call @editorialbot check references to check them again.

[Bios4Biol]

Submitting author: @SarahMaman (MAMAN Sarah) Repository: https://forgemia.inra.fr/bios4biol/intronseeker Branch with paper.md (empty if default branch): master Version: v1.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78"><img src="https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78/status.svg)](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78)

Author instructions

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

@SarahMaman 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:

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Please find below my suggestion for potential reviewers:
Erwan Core
https://www.sb-roscoff.fr/fr/corre-erwan/798
Patrick Durand
https://annuaire.ifremer.fr/cv/24218/

Thank you,
Sarah Maman

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1186/1471-2105-15-293 is OK
- 10.1038/nsmb.2143 is OK
- 10.1038/s41477-020-0688-1 is OK
- 10.1101/gr.177790.114 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1038/nmeth.3317 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.1093/nar/gks251 is OK
- 10.1038/nmeth.3176 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@SarahMaman The DOI issues seem to be resolved now. I will now be looking for a handling editor. Note however that many editors are busy handling other submissions. I've therefore waitlisted this submission for now. We will assign an editor as soon as one becomes available.

[Kevin-Mattheus-Moerman]

@editorialbot invite @kellyrowland as editor

[editorialbot]

Invitation to edit this submission sent!

[kellyrowland]

@Kevin-Mattheus-Moerman I can take this on as editor.

[Kevin-Mattheus-Moerman]

@editorialbot assign @kellyrowland as editor

[editorialbot]

Assigned! @kellyrowland is now the editor

[kellyrowland]

hi @greatfireball @warrenlr 👋 would you be interested in and available to review this JOSS submission?

[kellyrowland]

hi @edifice1989 @druvus 👋 would you be interested in and available to review this JOSS submission?

[kellyrowland]

hi @andrewjpage @kapsakcj @azneto 👋 would you be interested in and available to review this JOSS submission?

[andrewjpage]

Sorry this is beyond my area of expertise.

[kapsakcj]

^ Same goes for me, this is beyond my expertise so I would not feel comfortable reviewing. I will ask around and see if I can find any potential reviewers

[kellyrowland]

no problem, thanks for the quick responses. any referrals for potential reviewers would be hugely appreciated!

[kellyrowland]

hello @tkchafin @natir @CFGrote 👋 would you be interested in and available to review this JOSS submission? if not, could you recommend any potential reviewers?

[CFGrote]

Yes, can do

[tkchafin]

Yeah I can do it

[natir]

So I assume you didn't need me ?

[kellyrowland]

I suppose not @natir but thanks for checking in. 😅

[kellyrowland]

@editorialbot add @CFGrote as reviewer

[editorialbot]

@CFGrote added to the reviewers list!

[kellyrowland]

@editorialbot add @tkchafin as reviewer

[editorialbot]

@tkchafin added to the reviewers list!

[kellyrowland]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6272.