Mothur¶
Mothur seeks to develop a single piece of open-source, expandable software
to fill the bioinformatics needs of the microbial ecology community. It
currently incorporates the functionality of dotur, sons, treeclimber,
s-libshuff, unifrac, and more. In addition to improving the flexibility
of these algorithms, Mothur has added a number of other features including
calculators and visualisation tools.
Mothur is available as a module on Apocrita.
Usage¶
To run the default installed version of Mothur, simply load the mothur module:
module load mothur
then run one of the Mothur commands such as
mothur inputfile.mothur
Multiple-processor commands¶
The following mothur commands can take advantage of multiple processors:
| Commands | |||
|---|---|---|---|
| align.seqs | chimera.bellerphon | chimera.ccode | chimera.check |
| chimera.pintail | chimera.slayer | chimera.uchime | classify.seqs |
| cluster.split | dist.seqs | dist.shared | filter.seqs |
| indicator | metastats | pairwise.seqs | parsimony |
| phylo.diversity | rarefaction.single | screen.seqs | summary.seqs |
| summary.shared | trim.seqs | unifrac.unweighted | unifrac.weighted |
To specify that multiple processors can be used, add the processors option to
a command. Once a mothur command has had the processors option set,
subsequent commands that allow the processors option will use the value
originally specified:
mothur > filter.seqs(fasta=gg_13_5_99.align, trump=., processors=4)
Example job¶
Serial job¶
Here is an example job running on 1 core and 2GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load mothur
mothur inputfile.mothur