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.

kbm2 2.5                                           April 2020                                            KBM2(1)