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Quick start for mothur users

See also
Downstream analysis in mothur

I am familiar with the basics of mothur; for example, I have run some of the commands  for benchmarking. But I am not an expert -- if any of the information on this page is wrong or out of date, please let me know and I will update it.

Recommended: Denoise or generate OTUs with USEARCH
UPARSE generates OTUs with better accuracy than mothur (see benchmark results).

UNOISE recovers the biological sequences in a sample by "denoising" (error-correction), giving better resolution than 97% OTUs. The denoised sequences can be considered OTUs and can be used to make an OTU table (see unoise command for details). I recommend denoising over making 97% OTUs in most cases. Mothur does not support denoising, at least through v.1.38.

Downstream analysis
Once you have made an OTU table, then you can use mothur (or QIIME) for downstream analysis: alpha and beta diversity, principle component analysis etc. USEARCH can generate OTU tables in mothur shared file format. This should give you everything you need to do the rest of your analysis in mothur. If it doesn't, I will add new features to USEARCH as needed -- just let me know.