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

[editorialbot]

Submitting author: !--author-handle-->@SarahMaman<!--end-author-handle-- (MAMAN Sarah) Repository: https://forgemia.inra.fr/bios4biol/intronseeker Branch with paper.md (empty if default branch): master Version: v1.0 Editor: !--editor-->@kellyrowland<!--end-editor-- 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.

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

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.41 s (203.2 files/s, 44531.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
HTML                             24            599            192           8340
Python                           10            460           1394           3029
Markdown                         31            854              0           2015
Perl                              2            151            150            362
Bourne Shell                      4             68             88            238
JavaScript                        6              0             70            179
TeX                               1             13              3            118
YAML                              2              4             16             40
CSS                               3              0              6              3
Bourne Again Shell                1              3             16              2
--------------------------------------------------------------------------------
SUM:                             84           2152           1935          14326
--------------------------------------------------------------------------------

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]

: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:

chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data Submitting author: @greatfireball Handling editor: @pjotrp (Retired) Reviewers: @jdeligt Similarity score: 0.8268

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.8182

A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments Submitting author: @mgalland Handling editor: @brainstorm (Retired) Reviewers: @vladsaveliev Similarity score: 0.8146

TipToft: detecting plasmids contained in uncorrected long read sequencing data Submitting author: @andrewjpage Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @ctb, @kapsakcj, @azneto Similarity score: 0.8111

LTRpred: de novo annotation of intact retrotransposons Submitting author: @HajkD Handling editor: @lpantano (Active) Reviewers: @dcassol, @mdozmorov Similarity score: 0.8110

⚠️ 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]

@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? :point_up: 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:

@editorialbot commands

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 https://github.com/openjournals/joss-reviews/issues/6272.