CowPi consists of a set of pre-calculated files that can be used with an installation of PICRUSt to allow functional predictions to be made from 16S rRNA samples from the rumen microbiome.
All pre-calculated files are freely available under a Creative Commons Licence to allow researchers to implement CowPi in their own instance of Galaxy using PICRUSt. If you do this, we request if possible that researchers make a version of CowPi available to the wider rumen microbial community and to let us know so we can add their galaxy implementation here.
An implementation of CowPi has been made publicly available by Aberystwyth University at: https://share-galaxy.ibers.aber.ac.uk/
CowPi uses
- A phylogenetic trees constructed from all 16S rRNA OTUs from the Global Rumen Census combined with the 16S rRNA sequences from 500 cultured rumen microbes from the Hungate 1000 project.
- Abundances of genes coding for different functions collection as defined by Kegg orthologs from the full genome sequences of 497 genomes from the rumen, including those from Hungate 1000 .
For more information on the rationale and usage (including tutorials), please see the menu on the right.
CowPi how now been published in Frontiers in Microbiology here: https://www.frontiersin.org/articles/10.3389/fmicb.2018.01095/full
The full citation for the paper is:
Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A., Siu Ting, K., Hughes, M., Rubino, F., Friedersdorff, M. and Creevey, C., 2018. CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software. Frontiers in Microbiology, 9, p.1095.
The full citation for the paper is:
Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A., Siu Ting, K., Hughes, M., Rubino, F., Friedersdorff, M. and Creevey, C., 2018. CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software. Frontiers in Microbiology, 9, p.1095.
All data from behind CowPi is available under a Creative commons licence on Zenodo here:
