using mothur's rarefaction module with external data?

I’m currently working to add features to a pipeline already in service at my institution. I’m particularly interested in the rarefaction commands of mothur. I’d like to know if it is possible to use these commands with external data. For instance, if I properly format a OTU table output coming from another script/software and type something like rarefaction(

yeah sure. from the command line you could run something like…

mothur “#rarefaction.single(shared=myOTUtable.shared)”

The shared input file would of course have to be in the correct format.


Great it works thanks!