---
name: "kbm2"
section: "1"
platform: "linux"
package: "wtdbg2"
version: "2.5-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kbm2"
---

# kbm2(1)

simple instance which implemented kmer-binmap

## 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.