PAN and CORE genome analysis

[shashankgupta]

Hi,
I have an OTU biom file (obtained from Closed reference QIIME 1.8.0 v) contains 65 samples, I am trying to do analysis for PAN/CORE genome.
I have filtered out the taxonomy from the abundance file (with particular threshold, lets say 60 %), now i have an taxonomy column only in file from all the 65 samples (with threshold 60%), Is there is a way where i can do the functional annotation for it ?

Any server/ software is there which can do that ?

Any suggestions ?

Best !
Shashank

[diego diaz]

Hi,

I think you did 16S sequencing. If that is the case, maybe you are misunderstanding the meaning of CORE / PAN genome.

CORE genome is the set of genes shared by all your organisms. PAN genome is the CORE genome plus the accessory genome. To build a CORE or PAN genome you have to have the gene sequences of your organisms. In 16S analysis you only get the 16S ribosomal RNA, you don't have the sequences of the genes.

There are some tools to predict functional content based on 16S reads, like picrust https://picrust.github.com/picrust/