Mothur 2016

Introduction

Mothur "seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. mothur is available under the GPL license." ¹

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• Mothur/1.48.0-foss-2019b-Python-3.7.4

Loading Mothur

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load Mothur

Always remember: these commands are case-sensitive!

Using Mothur

After loading Mothur with module load Mothur, you have access to the binary file mothur which can be used in various ways. To use Mothur interactively just type in `mothur` and the prompt will change to mothur > . Within this Mothur shell, you can type in commands like this:

mothur > make.file(inputdir=., type=fastq, prefix=stability)

... where mothur > must not be typed in as part of the command, but symbolizes the Mothur command prompt.

But on the cluster, it is more likely and highly advised to use either the batch mode or the command line mode. You can use the command line mode to insert any Mothur command you need into your slurm job script and submit it to one of the compute nodes as it is usual practice in our cluster environment. To do this, you can use the same command syntax as with the interactive mode, but you need to put the actual commands between double quotes and set a hash mark # at the beginning. So, instead of this command inside the interactive Mothur shell:

 mothur > make.file(inputdir=., type=fastq, prefix=stability)

... you would call the mothur executable and the appending commands as follows:

mothur "#make.file(inputdir=., type=fastq, prefix=stability)"
 

To get an overview of how to use Mothur you can just type in mother --help after loading the module to print out a help text to get you started:

$ mothur --help
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.48.0

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

mothur > help()

NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.


Clustering commmands include: cluster, cluster.classic, cluster.fit, cluster.split, mgcluster, phylotype

General commmands include: get.current, get.dists, make.biom, make.group, make.file, make.group, make.lefse, merge.count, merge.files, merge.groups, remove.dists, rename.file, set.current, set.dir, set.logfile, set.seed, system

Hypothesis Testing commmands include: amova, anosim, clearcut, cooccurrence, corr.axes, deunique.tree, homova, indicator, kruskal.wallis, libshuff, mantel, nmds, otu.association, parsimony, pca, pcoa, phylo.diversity, unifrac.unweighted, unifrac.weighted

OTU-Based Approaches commmands include: biom.info, classify.svm, collect.shared, collect.single, create.database, dist.shared, estimator.single, filter.shared, get.communitytype, get.coremicrobiome, get.group, get.groups, get.label, get.otus, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.sharedseqs, heatmap.bin, heatmap.sim, lefse, list.otus, list.otus, make.clr, make.shared, merge.otus, metastats, normalize.shared, otu.hierarchy, primer.design, rarefaction.shared, rarefaction.single, remove.groups, remove.otus, remove.otus, remove.rare, sens.spec, sparcc, split.abund, summary.shared, summary.single, tree.shared, venn

Phylotype Analysis commmands include: classify.otu, classify.seqs, classify.tree, get.lineage, merge.taxsummary, remove.lineage, summary.tax

Sequence Processing commmands include: align.check, align.seqs, bin.seqs, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, cluster.fragments, consensus.seqs, count.groups, count.seqs, degap.seqs, deunique.seqs, dist.seqs, fastq.info, filter.seqs, get.mimarkspackage, get.seqs, list.seqs, make.contigs, make.fastq, make.lookup, make.sra, count.seqs, merge.sfffiles, pairwise.seqs, pcr.seqs, pre.cluster, remove.seqs, rename.seqs, reverse.seqs, screen.seqs, seq.error, sff.multiple, sff.info, shhh.flows, shhh.seqs, sort.seqs, split.groups, sra.info, sub.sample, summary.qual, summary.seqs, trim.flows, trim.seqs, unique.seqs

For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'

[ ... ]

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki.

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.

mothur > quit()

Documentation

General information about Mothur and helpful links can be found on the GitHub project page. The full documentation can be found as a wiki here.