Difference between revisions of "Applications/Crop"
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==Usage== | ==Usage== | ||
| − | CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen. | + | CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at the University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen. |
CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate. | CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate. | ||
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</pre> | </pre> | ||
| − | See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on options used. | + | See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used. |
| − | == | + | ==Next Steps== |
* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP] | * [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP] | ||
Revision as of 16:52, 8 November 2022
Application Details
- Description:
- Version: 1.33 (compiled with gcc-6.3.0)
- Module: crop/1.33/gcc-6.3.0
- Licence: GNU
Usage
CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at the University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen.
CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011)
Module
[username@login01 ~]$ module add crop/1.33/gcc-6.3.0 [username@login01 ~]$ CROPLinux –i MyInput.fasta
See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used.
Next Steps