See also
mothur
"shared" file format
mothur "list"
file format
mothur "names" file
format
The starting point for downstream OTU analysis is an
OTU table giving the number of reads per sample per
OTU. This is all you need to perform many standard analyses including
rarefaction, alpha diversity and beta diversity.
The mothur term for an
OTU table is a "shared file". To get an OTU table in
mothur shared file format, use the
-mothur_shared_out option of the otutab command.
You may also need a tree for the OTUs, e.g. for
UniFrac analsysis as
implemented in the
unifrac.weighted and
unifrac.unweighted
commands in mothur. To make a tree, you can use the
cluster_agg command in usearch. For example:
usearch -cluster_agg otus.fa -treeout otus.tree
This generates a tree in Newick format which is compatible with mothur and many other programs. Some programs are very picky about labels in Newick files which may cause problems. To get the best compatibility with other software, you should update the sequence labels as follows. Delete any usearch-style annotations (things like size=123;). Make sure you use only letters and numbers, don't use anything else (even periods or underscores). Don't use labels longer than 10 characters. Labels like Otu123 should be compatible with most (all?) programs.
In the following examples I willl use the
command-line mode
of mothur. I'll assume the shared file is named shared.txt and is in the
current directory when you start mothur. After running a mothur command as
shown below, you should see the output files and a mothur log file in the
current directory.
Rarefaction
You can use the
rarefaction.single
command.
mothur "#rarefaction.single(shared=shared.txt)"
Alpha diversity
You can use the
summary.single
command.
mothur "#summary.single(shared=shared.txt)"
Beta diversity
You can use the
summary.shared
command.
mothur "#summary.shared(shared=shared.txt)"