.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH KBM2 "1" "April 2020" "kbm2 2.5" "User Commands"
.SH NAME
kbm2 \- simple instance which implemented kmer-binmap
.SH SYNOPSIS
.B kbm
\fI\,<options> \/\fR[\fI\,start|list|stop\/\fR]
.SH DESCRIPTION
Program: kbm is a simple instance which implemented kmer\-binmap
.IP
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
.PP
Version: 2.5 (20190621)
Author: Jue Ruan <ruanjue@gmail.com>
.SH OPTIONS
.HP
\fB\-i\fR <string> File(s) of query sequences, +, [STDIN]
.HP
\fB\-d\fR <string> File(s) of reference sequences, +, [<\-i>]
.TP
\fB\-L\fR <int>
Choose the longest subread and drop reads shorter than <int> (5000 recommended for PacBio) [0]
Negative integer indicate keeping read names, e.g. \fB\-5000\fR.
.HP
\fB\-o\fR <string> Output file, [STDOUT]
.TP
\fB\-I\fR
Interactive mode
e.g. `mkfifo pipe` then `while true; do cat pipe && sleep 1; done | kbm \fB\-t\fR 8 \fB\-I\fR \fB\-d\fR ref.fa \fB\-i\fR \- \fB\-Hk\fR 21 \fB\-S\fR 4`
then `cat 1.fq >pipe; cat 2.fq >pipe`, fastq format is better in interaction
.TP
\fB\-f\fR
Force overwrite
.TP
\fB\-t\fR <int>
Number of threads, 0: all cores, [1]
.TP
\fB\-k\fR <int>
Kmer\-f size, <= 23, [0]
.TP
\fB\-p\fR <int>
Kmer\-p size, <= 23, [21]
.TP
\fB\-K\fR <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
.TP
\fB\-E\fR <int>
Min kmer frequency, [1]
.TP
\fB\-O\fR <int>
Filter low complexity bins (#indexed_kmer less than <\-O>), [2]
.TP
\fB\-S\fR <float>
Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00]
\fB\-S\fR is very useful in saving memory and speeding up
please note that subsampling kmers will have less matched length
.TP
\fB\-B\fR <int>
Select no more than n seeds in a query bin, [256]
If you are using shared kbmidx by other process using \fB\-D\fR too, it will bring wrong behavior
.TP
\fB\-D\fR <int>
Strand of alignment, 1: forward, 2: reverse, 3: both, [3]
.TP
\fB\-X\fR <int>
Max number of bin(256bp) in one gap, [4]
.TP
\fB\-Y\fR <int>
Max number of bin(256bp) in one deviation, [4]
.TP
\fB\-Z\fR <float>
Max fraction of gapped BINs / aligned BINs, [0.6]
.TP
\fB\-x\fR <int>
penalty for BIN gap, [\-7]
.TP
\fB\-y\fR <int>
penalty for BIN deviation, [\-21]
.TP
\fB\-z\fR <int>
Enable refine alignment with \fB\-p\fR <\-z> [0]
.TP
\fB\-l\fR <int>
Min alignment length, [2048]
.TP
\fB\-m\fR <int>
Min matched length, [200]
.TP
\fB\-s\fR <float>
Min similarity, calculated by kmer matched length / aligned length, [0.05]
.TP
\fB\-r\fR <float>
Max length variation of two aligned fragments, [0.25]
.TP
\fB\-c\fR
Insist to query contained reads against all
.TP
\fB\-C\fR
Chainning alignments
.TP
\fB\-n\fR <int>
Max hits per query, [1000]
.TP
\fB\-T\fR <int>
For debug, [0]
.HP
\fB\-W\fR <string> Dump kbm index to file, [NULL]
.HP
\fB\-R\fR <string> Load kbm index from file, [NULL]
.TP
\fB\-q\fR
Quiet
.TP
\fB\-V\fR
Print version information and then exit
.PP
Server start: {kbm \fB\-R\fR <wt.fa.kbmidx> start}, will mmap wt.fa.kbmidx into mmeory
Server  list: {kbm \fB\-R\fR <wt.fa.kbmidx> list [10]}, will list the object tree in file
Server  stop: {kbm \fB\-R\fR <wt.fa.kbmidx> stop},  will remove the mmap object
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.