Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

CROP | A method of unsupervised Bayesian clustering

Provides a clustering tool that automatically determines the best clustering result for 16S rRNA sequences at different phylogenetic levels. Our study shows that CROP gives accurate clustering results, both in terms of the number of clusters and their abundance levels, for various types of 16S rRNA datasets. In contrast, the standard hierarchical clustering strategy, even with the preclustering process and the average linkage method, still frequently overestimates the number of operational taxonomic units (OTUs) in the presence of sequencing errors, resulting in an underestimation of the abundance level of the underlying OTUs. By applying our method to several datasets, we demonstrate that CROP is robust against sequencing errors and that it produces more accurate results than conventional hierarchical clustering methods.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

CROP forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

CROP classification

CROP specifications

Unique identifier:
OMICS_01442
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Computer skills:
Advanced
Maintained:
Yes
Name:
Clustering 16S rRNA for OTU Prediction
Interface:
Command line interface
Operating system:
Unix/Linux, Windows
License:
GNU General Public License version 2.0
Stability:
Stable

CROP distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

CROP support

Documentation

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Molecular and Computational Biology Program, Department of Biology, University of Southern California, Los Angeles, CA, USA; MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China

Funding source(s)

National Institutes of Health; Center of Excellence in Genomic Sciences (CEGS) 2P50 HG002790-06; National Science Foundation of China (60805010)

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.