I'm looking for a program for generating OTUs (as the title suggests!) which I will be able to incorporate into a pipeline I'm working on. I know RDP/Mothur is the holy sacrament for diversity work but I just want to extract the OTU generation portion.
Really, what I'm looking for is an output saying:
@1 PID: x OTUs
@2 PID: y OTUs
@3 PID: z OTUs etc
and then have a list with a representative sequence for each OTU at each PID for megablasting/databasing.
jMOTU covers all the bases, but its a java application so I cant integrate it. ( http://www.nematodes.org/bioinformatics/jMOTU/index.shtml )
All recommendations appreciated!
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written
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Daniel
Mothur will do this. http://www.mothur.org/wiki/Main_Page
In the end you'll get for different cluster distances (OTUs pariwise ditance of 0.01, 0.05, 0.1, etc), the number of otus found and the reads that fall into those otus.
pick one of the reads, or use the gapped read alignment to build your consensus sequence.
There are a lot of good examples on the mothur wiki to generate the OTUs.
And it's 'command-lineable'.
Don't forget to mention that MG-RAST uses it now too!
...but it's closed source
You can use CD-HIT to get representative sequences at a specified level of similarity
For example, 98% for "species" with 16S sequences.
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why can't you integrate it "because it's a java app" ?
Maybe I'm mistaken, but the only way I can use jMOTU is through the GUI and there's no command line interface to put into a script. Anything I am going to write is going to be perl though, as I have no java knowledge. Am I missing a trick?
ah ok, it's a gui problem, not a java problem.