Combine mothur and picrust

Integrating mothur with other programs
1

Picrust is a recent published tool that can infer biological pathways from 16S RNA. In spite that WGS seems better for this purpose, it still shows additional information. (Picrust:Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Langille, M. G.I.; Zaneveld, J.; Caporaso, J. G.; McDonald, D.; Knights, D.; a Reyes, J.; Clemente, J. C.; Burkepile, D. E.; Vega Thurber, R. L.; Knight, R.; Beiko, R. G.; and Huttenhower, C. Nature Biotechnology, 1-10. 8 2013.)

I’m using mothur and get an OTU table together with a taxonomy file. Picrust needs a .biom file which comes from qiime. I found a make.biom() command, and transfer the OTUs with their taxonomy info to a .biom file and passed it to picrust, but got an empty result. After examine the .biom I got with the one in .picrust’s tutorial, I found the structure is different. Another issue is that abudance of each OTU is lost during the transfer.

Is there any covenient way to deal with this? Or add a new command in the next version?

Thank you!

2

Although mothur’s make.biom command makes a biom file, the picrust program’s biom file is a bit more restrictive. Picrust expects Greengenes OTUIDs to be in the biom file. In our next version, we are adding picrust and reftaxonomy parameters to the make.biom command to accommodate these requirements.