cdhit-454 - Online in the Cloud

PROGRAM:

NAME

cd-hit-454 - quickly group sequences, optimised for 454 data

SYNOPSIS

cdhit-454 [Options]

DESCRIPTION

====== CD-HIT version 4.6 (built on Jan 23 2016) ======

Options

-i input filename in fasta format, required

-o output filename, required

-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 memory limit (in MB) for the program, default 800; 0 for unlimitted;

-T number of threads, default 1; with 0, all CPUs will be used

-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

-match matching score, default 2

-mismatch
mismatching score, default -1

-gap gap opening score, default -3

-gap-ext
gap extension score, default -1

-bak write backup cluster file (1 or 0, default 0)

-h print this help

Questions, bugs, contact Weizhong Li at [email protected]

If you find cd-hit useful, please kindly cite:

"Clustering of highly homologous sequences to reduce thesize of large protein
database", Weizhong Li, Lukasz Jaroszewski & Adam Godzik. Bioinformatics, (2001)
17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of
protein or nucleotide sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006)
22:1658-1659 "Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li. Artificial and
natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics
(2010) 11:187

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