Gbk files

[Bury-Mone]

Hello,

Thank you for designing this pipeline, which is really easy for non-experts to use. I have a small question. Is there an option to retrieve annotated genomes in gbk format?
Thank you for this information.

Have a nice summer,
Stéphanie

[axbazin]

Hello,

Thank you!
There is no option currently, but we did talk about adding this for the next release as it would definitely be much more practical.

Currently, the closest output files to GBK format are the 'projection' files, which stores basic information that you will commonly find in gbk file, but in a tsv format (so not very practical to use directly with other tools I'm afraid). See the projection wiki section if that may get you what you are looking for.

Have a nice summer too,
Adelme

[Bury-Mone]

I thank you so much for this information.
All the best,
Stéphanie

[jpjarnoux]

Hi, we have included the option to export the pangenome annotation in GFF format. It's not yet in GBK format, but it's closer than a TSV file. The option is not yet available in the main release. You can either wait for the next release or use the development branch.
NB: With the next branch, the pangenome file model will change, requiring you to rebuild your pangenome.

[Bury-Mone]

Bonjour, Je vous remerciebeaucoup pour votre réponse et cette adaptation très utile de PPANGGOLIN. Très bonne continuation, Amicalement Stéphanie De: "Jérôme Arnoux" ***@***.***> À: "labgem/PPanGGOLiN" ***@***.***> Cc: "Bury-Moné Stéphanie" ***@***.***>, "Author" ***@***.***> Envoyé: Vendredi 27 Octobre 2023 10:03:30 Objet: Re: [labgem/PPanGGOLiN] Gbk files (Issue #128) Hi, we have included the option to export the pangenome annotation in GFF format. It's not yet in GBK format, but it's closer than a TSV file. The option is not yet available in the main release. You can either wait for the next release or use the [ https://github.com/labgem/PPanGGOLiN/tree/dev | development branch ] . NB: With the next branch, the pangenome file model will change, requiring you to rebuild your pangenome. — Reply to this email directly, [ #128 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AK6BFKYLFOHUKCYVF4KR5MTYBNTFFAVCNFSM6AAAAAA3IP7J5SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBSGQ3TONRWGM | unsubscribe ] . You are receiving this because you authored the thread. Message ID: <labgem/PPanGGOLiN/issues/128/1782477663 @ github . com>