Applications/Crop

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)

Interactive Session


[username@login01 ~]$ interactive
salloc: Granted job allocation 3619731
Job ID 3619731 connecting to c081, please wait...
c081.vc-main

[username@c081 ~]$ module add crop/1.33/gcc-6.3.0
[username@c081 ~]$ CROPLinux –i MyInput.fasta

Batch Script

#!/bin/bash
#SBATCH -J jobname                # Job name, you can change it to whatever you want
#SBATCH -n 4                      # Number of cores 
#SBATCH -o %N.%j.out              # Standard output will be written here
#SBATCH -e %N.%j.err              # Standard error will be written here
#SBATCH -p compute                # Slurm partition, where you want the job to be queued 
#SBATCH -t=20:00:00               # Run for 20 hours
#SBATCH --mail-user=your email    # Mail to email address when finished

module purge
module add crop/1.33/gcc-6.3.0
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.