Jacques Dainat

We might change this order but I guess it will be only esthetic. I mean the change will affect the order in EMBL flat file but I don't think it...

If order matter yes you should upload an AGP file. See the dedicated section in the ENA help: https://ena-docs.readthedocs.io/en/latest/submit/fileprep/assembly.html#agp-file and NCBI https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ and examples at the bottom as here: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/scaffold_from_contig_WGS.agp.v2.0/...

I got an answer: Order matter: ``` The accession numbers will be assigned to the sequences in the exact order it was included in the flat file submission. ``` So...

@ireneortega I would need some feedbacks from you to close this issue. I have tried on my side and EMBLmyGFF3 v2.1 sounds to work as expected. Did you use an...

Ok then it wiould be fixed if you install python >=3.6 ``` Since Python 3.6, the default dict class maintains key order, meaning this dictionary will reflect the order of...

Try with branch 2.2. 1) Git clone the repo 2) move into the 2.2 branch (`git checkout 2.2`) 3) There is a conda file you can use to prepare the...

Are you sure you use the correct coordinate system? How this gff has been generated?

Any update from your side? Could you share the data?

Good catch, indeed you should be able to use those option for as many publication you would like to include. We will have a look at it and fix that...

I do not have such script and I do not know any in particular, but I'm sure you can figure out by googling. At least N50 will not change, but...