THE CROP WIKI

Introduction

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 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)

Please refer to the User Guide included in the repository for usage information.

This project is currently maintained by Yichao Dong, a graduate student in Prof. Ting Chen's lab.

If you have any questions regarding the usage of CROP, please email us at yichaodo@usc.edu

FAQ

1. On what systems can I run CROP on?

CROP is written in C++, so it can be compiled and run in multiple platforms that has an up-to-date C++ compiler, for example, on a Linux distribution, Mac OS X and etc.

2. How do I get the program to run?

CROP is a compiled program and it only runs in a terminal environment. For example in Linux, you have to use terminal to navigate to the project source code fold and compile the project first by typing the command "make" in your terminal, after compilation, you will see a executable called "CROPLinux". To get the program running. For more about parameter setting, please refer to the User Guide document.

3. I have trouble compiling CROP, what should I do?

If you fail to compile CROP on your machine, most probably it is due to the lack of GSL library. Please intall a GSL library first on your machine before compiling CROP.