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CD-HIT-EST-2D(1) User Commands CD-HIT-EST-2D(1)

NAME

cd-hit-est-2d - run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format

SYNOPSIS

cd-hit-est-2d [Options]

DESCRIPTION

====== CD-HIT version 4.7 (built on Jun 14 2017) ======

Options

input filename for db1 in fasta format, required
input filename for db2 in fasta format, required
input filename in fasta/fastq format for R2 reads if input are paired end (PE) files

-i db1-R1.fq -j db1-R2.fq -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2 or

-i db1-R1.fa -j db1-R2.fa -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2

output filename, required
output filename for R2 reads if input are paired end (PE) files
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
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
band_width of alignment, default 20
memory limit (in MB) for the program, default 800; 0 for unlimitted;
number of threads, default 1; with 0, all CPUs will be used
word_length, default 10, see user's guide for choosing it
length of throw_away_sequences, default 10
length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
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
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
length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 0.9, seqs in db1 may just >= 90% seqs in db2
length difference cutoff, default 0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 60, seqs in db2 may 60aa longer than seqs in db1
alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
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
alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
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
minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
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
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
maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases
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 !!
input paired end (PE) reads, default 0, single file if set to 1, please use -i R1 -j R2 to input both PE files
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
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
1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
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
1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+ strand alignment
masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
matching score, default 2 (1 for T-U and N-N)
mismatching score, default -2

-gap gap opening score, default -6

gap extension score, default -1

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

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
June 2017 cd-hit-est-2d 4.6.7