NAME

       kbm2 - simple instance which implemented kmer-binmap

SYNOPSIS

       kbm <options> [start|list|stop]

DESCRIPTION

       Program: kbm is a simple instance which implemented kmer-binmap

              it  maps  query  sequence against reference by kmer matching matched kmer-pairs are
              bined (256bp) and counted in a matrix dynamic programming is  used  to  search  the
              best path

       Version: 2.5 (20190621) Author: Jue Ruan <ruanjue@gmail.com>

OPTIONS

       -i <string> File(s) of query sequences, +, [STDIN]

       -d <string> File(s) of reference sequences, +, [<-i>]

       -L <int>
              Choose  the longest subread and drop reads shorter than <int> (5000 recommended for
              PacBio) [0] Negative integer indicate keeping read names, e.g. -5000.

       -o <string> Output file, [STDOUT]

       -I     Interactive mode e.g. `mkfifo pipe` then `while true; do cat pipe && sleep 1;  done
              |  kbm  -t  8 -I -d ref.fa -i - -Hk 21 -S 4` then `cat 1.fq >pipe; cat 2.fq >pipe`,
              fastq format is better in interaction

       -f     Force overwrite

       -t <int>
              Number of threads, 0: all cores, [1]

       -k <int>
              Kmer-f size, <= 23, [0]

       -p <int>
              Kmer-p size, <= 23, [21]

       -K <float>
              Filter high frequency kmers, maybe repetitive, [1000] if K >= 1, take  the  integer
              value  as  cutoff,  MUST  <=  65535 else, mask the top fraction part high frequency
              kmers

       -E <int>
              Min kmer frequency, [1]

       -O <int>
              Filter low complexity bins (#indexed_kmer less than <-O>), [2]

       -S <float>
              Subsampling kmers, 1/(<-S>) kmers are indexed, [4.00] -S is very useful  in  saving
              memory  and  speeding  up please note that subsampling kmers will have less matched
              length

       -B <int>
              Select no more than n seeds in a query bin, [256] If you are using shared kbmidx by
              other process using -D too, it will bring wrong behavior

       -D <int>
              Strand of alignment, 1: forward, 2: reverse, 3: both, [3]

       -X <int>
              Max number of bin(256bp) in one gap, [4]

       -Y <int>
              Max number of bin(256bp) in one deviation, [4]

       -Z <float>
              Max fraction of gapped BINs / aligned BINs, [0.6]

       -x <int>
              penalty for BIN gap, [-7]

       -y <int>
              penalty for BIN deviation, [-21]

       -z <int>
              Enable refine alignment with -p <-z> [0]

       -l <int>
              Min alignment length, [2048]

       -m <int>
              Min matched length, [200]

       -s <float>
              Min similarity, calculated by kmer matched length / aligned length, [0.05]

       -r <float>
              Max length variation of two aligned fragments, [0.25]

       -c     Insist to query contained reads against all

       -C     Chainning alignments

       -n <int>
              Max hits per query, [1000]

       -T <int>
              For debug, [0]

       -W <string> Dump kbm index to file, [NULL]

       -R <string> Load kbm index from file, [NULL]

       -q     Quiet

       -V     Print version information and then exit

       Server  start:  {kbm  -R  <wt.fa.kbmidx> start}, will mmap wt.fa.kbmidx into mmeory Server
       list: {kbm -R <wt.fa.kbmidx> list [10]}, will list the object tree in file  Server   stop:
       {kbm -R <wt.fa.kbmidx> stop},  will remove the mmap object

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.