Paper was originally formatted for BMC Bioinformatics, but I think it may be worth submitting to:

GigaScience - Technical Note - https://academic.oup.com/gigascience/article/9/4/giaa025/5813097?searchresult=1

Another idea:

PLOS Computational Biology - Software - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007747

Galaxy papers are in:
9x Bioinformatics
4x Genome Research
3x Gigascience
3x Computational Biology
2x BMC Bioinformatics

Note: Two of the Gigascience papers were from the last 3 years (more recent). Lots of publications in Bioinformatics, though some of them are 2 page application notes.

I am leaning towards Gigascience, as you mentioned a positive experience with the journal.

Computational Biology may also be applicable, and I have published with PLOS previously.

Both journals have a similar impact factor. I don't think it will be difficult to reformat the paper for either journal.

[~aloraine] what are your thoughts?

I agree - let's go with Gigascience!

I have made a few changes to the paper to properly format it for GigaScience. The abstract is slightly reformatted with a few edits. Background/results is now under the heading Findings. Implementation is now under Methods, and is at the end of the paper. References have been updated to match GigaScience recommendations.

GigaScience requests individual figure files (Dropbox > IGB > Manuscripts > biovizConnect > figures).
The updated paper is in (Dropbox > IGB > Manuscripts > biovizConnect > gigaScience) along with a cover letter.

Assigning to [~aloraine] to submit the paper.

Technical Note instructions: https://academic.oup.com/gigascience/pages/technical_note

General instructions: https://academic.oup.com/gigascience/pages/instructions_to_authors

Submission site: https://www.editorialmanager.com/giga/default.aspx

Uploaded and submitted to GigaScience as a Technical Note. PDF from the GigaScience Web site is saved in the DropBox.