filtering 454 duplicate reads (cd-hit-454)

cd-hit-454 (http://weizhong-lab.ucsd.edu/cdhit_454/) identifies the duplicates from 454 reads, including exact duplicates and near identical duplicates. These duplicates are mostly sequencing artifacts in metagenomic samples, and therefore should be removed. However, most duplicates in transcriptomic reads are not artificial, so it is not suggested to run this program for transcriptomic datasets.

In this program, you can identify duplicates from 454 reads.
Inputs:
(1) DNA FASTA file (required)
(2) Email address (optional)
(3) Parameters (optional)
Outputs:
output.zip(including the following three files
(1) README.txt: description of the three output files
(2) output.1: Fasta file after removing artifacts
(3) output.1.clstr: Clusters with associated sequences (representative sequence in each cluster is ened with a "*")
Usage of web server:
(1) Select a DNA fasta file in user's local computer. (required)
(2) Fill in user's email adress. (optional)
(3) Fill in parameters. (optional, modifiy it according to user's requirement)
(4) Click "Submit" button. (required)
Sequence file to upload (required):
Email (optional):
Parameters
show description
    -c  sequence identity threshold, default 0.98
        this is a "global sequence identity" calculated as :
        number of identical amino acids in alignment
        divided by the full length of the shorter sequence + gaps
    -b  band_width of alignment, default 10
    -M  max available memory (Mbyte), default 1000
    -n  word_length, default 10, see user's guide for choosing it
    -aL alignment coverage for the longer sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AL alignment coverage control for the longer sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues
    -aS alignment coverage for the shorter sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AS alignment coverage control for the shorter sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues
    -B  1 or 0, default 0, by default, sequences are stored in RAM
        if set to 1, sequence are stored on hard drive
        it is recommended to use -B 1 for huge databases
    -g  1 or 0, default 0
        by cd-hit's default algorithm, a sequence is clustered to the first
        cluster that meet the threshold (fast cluster). If set to 1, the program
        will cluster it into the most similar cluster that meet the threshold
        (accurate but slow mode)
        but either 1 or 0 won't change the representatives of final clusters
    -D  max size per indel, default 1
EXAMPLE
Sequence file to upload (required): input.fasta
Email (optional): you@example.com
Parameters -c 0.98 -D 1
show description
    -c  sequence identity threshold, default 0.98
        this is a "global sequence identity" calculated as :
        number of identical amino acids in alignment
        divided by the full length of the shorter sequence + gaps
    -b  band_width of alignment, default 10
    -M  max available memory (Mbyte), default 1000
    -n  word_length, default 10, see user's guide for choosing it
    -aL alignment coverage for the longer sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AL alignment coverage control for the longer sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues
    -aS alignment coverage for the shorter sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AS alignment coverage control for the shorter sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues
    -B  1 or 0, default 0, by default, sequences are stored in RAM
        if set to 1, sequence are stored on hard drive
        it is recommended to use -B 1 for huge databases
    -g  1 or 0, default 0
        by cd-hit's default algorithm, a sequence is clustered to the first
        cluster that meet the threshold (fast cluster). If set to 1, the program
        will cluster it into the most similar cluster that meet the threshold
        (accurate but slow mode)
        but either 1 or 0 won't change the representatives of final clusters
    -D  max size per indel, default 1
Show an example
Submitting......
Program/Database References
1. "Artificial and natural duplicates in pyrosequencing reads of metagenomic data", Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li BMC Bioinformatics (2010) 11:187doi:10.1186/1471-2105-11-187.
Program/Database Version
Program: cd-hit-454 4.5.3
Database: N/A