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

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 4.8.1 (built on Aug 20 2021) ======

       Options

       -i     input filename for db1 in fasta format, required, can be in .gz format

       -i2    input filename for db2 in fasta format, required, can be in .gz format

       -j, -j2
              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

       -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

       -s2    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

       -S2    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

       -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

       -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)

       -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