Provided by: cd-hit_4.6.8-1_amd64 
NAME
cd-hit-est - run CD-HIT algorithm on RNA/DNA sequences
SYNOPSIS
cd-hit-est [Options]
DESCRIPTION
====== CD-HIT version 4.7 (built on Jul
1 2017) ======
Options
-i input filename in fasta format, required
-j input filename in fasta/fastq format for R2 reads if input are paired end (PE)
files
-i R1.fq -j R2.fq -o output_R1 -op output_R2 or
-i R1.fa -j R2.fa -o output_R1 -op output_R2
-o output filename, required
-op output filename for R2 reads if input are paired end (PE) files
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global
sequence identity" calculated as: number of identical amino acids in alignment
divided by the full length of the shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence
identity, calculated as : number of identical amino acids in alignment divided by
the length of the alignment NOTE!!! don't use -G 0 unless you use alignment
coverage controls see options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-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
-l length of throw_away_sequences, default 10
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta
defline and stops at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to
be at least 90% length of the representative of the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length
difference between the shorter sequences and the representative of the cluster can
not be bigger than 60
-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
-A minimal alignment coverage control for the both sequences, default 0 alignment must
cover >= this value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1,
the unmatched region (excluding leading and tailing gaps) must not be more than 10%
of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1,
the unmatched region (excluding leading and tailing gaps) must not be more than 10%
of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region
(excluding leading and tailing gaps) must not be more than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence
are stored on hard drive !! No longer supported !!
-P input paired end (PE) reads, default 0, single file if set to 1, please use -i R1
-j R2 to input both PE files
-cx length to keep after trimming the tail of sequence, default 0, not trimming if set
to 50, the program only uses the first 50 letters of input sequence
-cy length to keep after trimming the tail of R2 sequence, default 0, not trimming if
set to 50, the program only uses the first 50 letters of input R2 sequence e.g. -cx
100 -cy 80 for paired end reads
-ap alignment position constrains, default 0, no constrain if set to 1, the program
will force sequences to align at beginings when set to 1, the program only does +/+
alignment
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-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
-r 1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+
strand alignment
-mask masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
-match matching score, default 2 (1 for T-U and N-N)
-mismatch
mismatching score, default -2
-gap gap opening score, default -6
-gap-ext
gap extension score, default -1
-bak write backup cluster file (1 or 0, default 0)
-sc sort clusters by size (number of sequences), default 0, output clusters by
decreasing length if set to 1, output clusters by decreasing size
-sf sort fasta/fastq by cluster size (number of sequences), default 0, no sorting if
set to 1, output sequences by decreasing cluster size
-h print this help
Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu
For updated versions and information, please visit: http://cd-hit.org
cd-hit web server is also available from http://cd-hit.org
If you find cd-hit useful, please kindly cite:
"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 "CD-HIT: accelerated for clustering the next generation sequencing
data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics,
(2012) 28:3150-3152