Pan genome for fungal genomes

[bhanusakhamuri]

Does roary work for fungal genomes that are annotated?

[andrewjpage]

No. Further info in the FAQ http://sanger-pathogens.github.io/Roary/

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On Thu, 11 Oct 2018, 17:23 bhanusakhamuri, ***@***.***> wrote: Does roary for fungal genomes that are annotated? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#425>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV6SG8L-RxwoJqiK7MJYXw0f0Lxs8ks5uj3BygaJpZM4XX6CO> .

[tseemann]

If roary supported Genbank files it will be trivial to add support, one would just use $cds->spliced_seq->translate() to get the proteins.

[andrewjpage]

If you want to submit a pull request I would be happy to accept.

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On Sat, 13 Oct 2018, 05:38 Torsten Seemann, ***@***.***> wrote: If roary supported Genbank files it will be trivial to add support, one would just use $cds->spliced_seq->translate() to get the proteins. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#425 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV5DqibMlXD1zQ1hKlO0FClZf2Q5Aks5ukW4_gaJpZM4XX6CO> .

[Rob-murphys]

@tseemann Did you ever happen to do this? Currently looking for a tool to get fungal pan/core genomes

[teddyaroca]

This would be quite the useful feature that is not available elsewhere. I looked around and there are not good options to do this with fungal genomes. Same goes for annotations/gene predictions.