Provided by: cd-hit_4.8.1-4_amd64 bug

NAME

       cd-hit-est - run CD-HIT algorithm on RNA/DNA sequences

SYNOPSIS

       cd-hit-est [Options]

DESCRIPTION

              ====== CD-HIT version 4.8.1 (built on Aug 20 2021) ======

       Options

       -i     input filename in fasta format, required, can be in .gz format

       -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 or bases 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 or bases 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 this can be very slow if  the
              input is in .gz format

       -h     print this help

              Questions,  bugs,  contact  Weizhong  Li  at liwz@sdsc.edu For updated versions and
              information, please visit: http://cd-hit.org

              or https://github.com/weizhongli/cdhit

              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