Denoising such as IPED?

It would be totally killer if mothur could...
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Lethe
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Joined: Mon Jul 02, 2012 3:10 pm

Denoising such as IPED?

Post by Lethe » Wed Feb 21, 2018 4:00 am

Dear mothur creators,

thank you for your great program.

I wanted to ask if it would be able to add some "real" denoising command into mothur? It is partially because I am a bit interested in 100%ID OTUs and I am not sure if such analysis in mothur makes sense so far.
To be more particular, I had IPED on my mind, also because it is already based on mothur. Or at least, in this particular case, would it be possible for make.contigs to produce at least IPED compatible quality file?
However, I am not an expert on which denoising method works best, so I am open to other possibilities as well :)

Thanks!

pschloss
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Re: Denoising such as IPED?

Post by pschloss » Mon Feb 26, 2018 1:39 pm

In our testing, we have yet to see anything that is better than what we get out of make.contigs. You are free to not run pre.cluster, but like I said, I'm not convinced that anything has a better error rate. Also, you should know that by using a 100% similarity threshold, you are likely to split multiple rrn copies from the same genome into separate OTUs.

Pat

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