OTU finder (cd-hit-otu)

This program performs Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, we do OTU clustering at different distanct cutoffs (0.01, 0.02, 0.03... 0.12).

Please consult CD-HIT-OTU web site for detailed description of CD-HIT-OTU.

The whole CD-HIT-OTU program was zipped into one file and can be downloaded here

Currently we have only implemented CD-HIT-OTU server/service for 454 reads. If you want to process illumina reads, you can eithor download software or contact us.

Inputs:
(1) 454 rRNA FASTA file with primer included (required)
(2) Email address (optional)
Outputs:
output.zip(including the following fifteen files
(1) README.txt: description of the fifteen output files
(2) output.1: OTU results by different distance cutoffs
(3) otu.dist_0.01.txt: OTU and corresponding sequences at distance cutoff=0.01
(4) otu.dist_0.02.txt: OTU and corresponding sequences at distance cutoff=0.02
(5) otu.dist_0.03.txt: OTU and corresponding sequences at distance cutoff=0.03
(6) otu.dist_0.04.txt: OTU and corresponding sequences at distance cutoff=0.04
(7) otu.dist_0.05.txt: OTU and corresponding sequences at distance cutoff=0.05
(8) otu.dist_0.06.txt: OTU and corresponding sequences at distance cutoff=0.06
(9) otu.dist_0.07.txt: OTU and corresponding sequences at distance cutoff=0.07
(10) otu.dist_0.08.txt: OTU and corresponding sequences at distance cutoff=0.08
(11) otu.dist_0.09.txt: OTU and corresponding sequences at distance cutoff=0.09
(12) otu.dist_0.1.txt: OTU and corresponding sequences at distance cutoff=0.1
(13) otu.dist_0.11.txt: OTU and corresponding sequences at distance cutoff=0.11
(14) otu.dist_0.12.txt: OTU and corresponding sequences at distance cutoff=0.12
(15) output.2: output message for OTU determination
Usage of web server:
(1) Use mouse to click "Browse" button. Select the DNA fasta file in user's local computer. Click "open" button. (required)
(2) Fill in user's email adress. (optional)
(3) Click "Submit" button. (required)
Sequence file to upload (required):
Email (optional):
Parameters
show description
    -e  estimated error rate per base (default=0.0025)
        original 454 sequences: 0.5%
        after filtering low-quality sequences: 0.25%
EXAMPLE
Sequence file to upload (required): input.fasta
Email (optional): you@example.com
Parameters -e 0.0025
show description
    -e  estimated error rate per base (default=0.0025)
        original 454 sequences: 0.5%
        after filtering low-quality sequences: 0.25%
Show an example
Submitting......
Program/Database References
1. "Ultrafast Clustering Algorithms for Metagenomic Sequence Analysis", W. Li, L. Fu, B. Niu, S. Wu & J. Wooley Briefings in Bioinformatics, (2012) 13 (6):656-668. doi: 10.1093/bib/bbs035
2. "WebMGA: a Customizable Web Server for Fast Metagenomic Sequence Analysis", S. Wu, Z. Zhu, L. Fu, B. Niu & W. Li BMC Genomics 2011, 12:444. PDF Pubmed Citations
Program/Database Version
Program: cd-hit-otu-454 0.0.2
Database: N/A