Forum:How to acknowledge in the paper a reference genome that hasn't been published yet?

Question

[ciemanek]

My question is a less technical one, but I was not sure where to seek advice. I am currently working on a paper regarding variants called from DNA-seq, but the reference genome that was used for calling variants hasn't been published yet (I mean the whole pipeline for assembling scaffolds and annotating them). How should it be approached in the paper?

[h.mon]

By not published, you mean there is no paper, but it is available for download? Or it is not published and also not available? If the genome is available on the internet, you can reference the link.

Was the genome assembly and annotation performed by you or your research group? Another group made it available to you?

[ciemanek]

There is no paper regarding this particular genome and it is not available for download to the best of my knowledge. It was assembled by people I collaborate with, but as far as I understood their idea is to publish it in another paper in some time. The only information I have is that it was assembled using the same method they presented in their recent paper. I must admit I am confused on how to approach this :)

[h.mon]

It was assembled by people I collaborate with, but as far as I understood their idea is to publish it in another paper in some time.

First of all, be sure you have their permission to publish data based on their genome.

However, you may have a problem in your hands, as 1) I guess some reviewers would like / demand the genome at hand to be available, 2) providing variants without a reference genome isn't very helpful.

Answer 1

[GenoMax]

I see three options:

• Put the reference genome in GenBank, get an accession number and refer it in your paper. Provide correct attribution to those who did the work and put it together and say that method/analysis of the genome will be published independently.
• Wait until collaborators are ready to publish their paper/assembly and send both papers in at the same time. If you are not submitting to the same journal as they are, then you may need to include a copy of their manuscript with yours (to convince your reviewers that genome you used is legit/reasonably put together).
• Find a journal that does not require submission of reference sequence (there are some industrial biotech journals that don't require this since industrial strains may be patented etc, last I knew about this from several years back) and try your luck there (if your analysis fits in the scope of such journals, of course).

[WouterDeCoster]

And a fourth option may be that the other group publishes their paper describing the new reference genome as a preprint on bioRxiv. As such you can reference that paper and they can still submit their paper to a ""real"" journal.