Picrust 2 reference alignment

[Felipe Melis]

Hello All,

I was trying to generate a new database for Picrust 2, and I was wondering how you generate the reference alignment? Do you have a special approach or something?

I wasn't able to generate an alignment as short as the one provided by the default files.

Best regards

[Robyn Wright]

Hi there,

 

Can you be a bit more specific about what you’re doing please (the genomes you are using, which gene(s) you are creating an alignment using, etc)? The default files are created using only the 16S rRNA gene from the reference genomes, and not the entire genomes, in case this helps.

 

Best wishes,

Robyn

 

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[Felipe Melis]

I think my messages get deleted.

I use one 16S from IMG for each bacteria and archaea.

Thanks

[Robyn Wright]

I'm afraid that without knowing some more details about what you're using etc. then I don't know why they would be different. But, the genomes used for PICRUSt2 are from IMG, so I'm not sure if this is entirely necessary? 

Also, in case it is useful, I am currently working on updating the database used for PICRUSt2 to use the GTDB genomes - these already have a tree and would allow regular re-annotation, searching of them using custom HMM's, etc. 

Robyn

[Felipe Melis]

Ok, I understand!

Wow, about the new reference, can I offer help with that? I'm very interested in that database.

Regards