mOTU

Description

motu website

mOUT is a method that uses marker genes for taxonomic profiling of metagenomes. Phylogenetic markers are genes that can be used to reconstruct the evolutionary history of organisms and to profile the taxonomic composition of environmental samples. Efforts to find a good set of protein-coding phylogenetic marker genes (Ciccarelli et al., Science, 2006; Sorek et al., Science, 2007) led to the identification of 40 universal marker genes (MGs). These 40 MGs occcur in single copy in the vast majority of known organisms and they have recently been used to delineate prokaryotic organisms at the species level (Mende et al., 2013).

Environment Modules

Run module spider motu to find out what environment modules are available for this application.

Environment Variables

• HPC_MOTU_DIR - installation directory
• HPC_MOTU_BIN - executable directory
• HPC_MOTU_DOC - documentation directory

Additional Usage Information

Before running ruMOCAT.sh, please copy the MOCAT config from $HPC_MOCAT_CONF/MOCAT.cfg to your working directory and adjust it accordingly.

cp $HPC_MOCAT_CONF/MOCAT.cfg /path/to/your/desired/directory

Citation

If you publish research that uses motu you have to cite it as follows:

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., … Bork, P. (2013). Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 10(12), 1196–1199. https://doi.org/10.1038/nmeth.2693

Categories

biology, genomics