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)

    -e  estimated error rate per base (default=0.0025)
        original 454 sequences: 0.5%
        after filtering low-quality sequences: 0.25%

    -e  estimated error rate per base (default=0.0025)
        original 454 sequences: 0.5%
        after filtering low-quality sequences: 0.25%