Description Usage Arguments Details Value
Assign taxonomic paths to unclassified SSU rRNA sequences, by executing classify.seqs
in Mothur with the 'Wang' approach.
1 2 |
fasta |
a fasta file of rRNA sequences to be assigned with taxonomies, e.g. a set of sequences picked as the representatives of OTUs. |
template |
a faste file of rRNA reference sequences, default to download "Silva_119_provisional_release.zip" under "qiime" directory from SILVA archive under , and extract "Silva_119_rep_set97.fna", a representative set of SILVA rRNA references of version119 at 97% sequence identity. |
taxonomy |
a taxonomic path file mapping to the template file, default to load "Silva_119_rep_set97.fna" matched "taxonomy" stored in the package. |
ksize, iters, cutoff, processors |
parameters used in Classify.seqs by Mothur. |
dir.out |
a directory where the assigned files were outputted, by default to create |
This function performs 'classify.seqs' by running Mothur in command line mode, hence the executable Mothur on your computer is needed. For unix users, the absolute path of Mothur should be added to the PATH environmental variable and exported. For Windows users, the executable Mothur with extension .exe is required under your disks.
two files under dir.out
, a *.taxonomy
file which contains a taxonomic path for each sequence and a *.tax.summary
file which contains a taxonomic outline indicating the number of sequences that were found at each level (kingdom to species).
a list containing the following components:
exitStatus an error code ('0' for success) given by the execution of the system Mothur commands, see system
.
stderr, stdout standard errors and outputs by executing Mothur command 'classify.seqs'.
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