Quick start for mothur users
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if any of the information on this page is wrong or out of date, please let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
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.
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 --