---
name: "kma"
section: "1"
platform: "linux"
package: "kma"
version: "1.4.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kma"
---

# kma(1)

maps and/or aligns raw reads to a template database

## NAME

kma - maps and/or aligns raw reads to a template database

## DESCRIPTION

-

  KMA-1.3.23 maps and/or aligns raw reads to a template database.

- Options:

  Desc:                                   Default:

-

  Input:

- **-i**

  Single end input(s)                     stdin

- **-ipe**

  Paired end input(s)

- **-int**

  Interleaved input(s)

-

  Output:

- **-o**

  Output prefix

- **-ef**

  Output additional features              False

- **-vcf**

  Output vcf file, 2 to apply FT          False

- **-sam**

  Output sam, 4/2096 for mapped/aligned   False

- **-nc**

  No consensus file                       False

- **-nc**

  No aln file                             False

- **-nf**

  No frag file                            False

- **-matrix**

  Output assembly matrix                  False

- **-a**

  Output all template mappings            False

- **-and**

  Use both mrs and p-value on consensus   or

- **-oa**

  Use neither mrs or p-value on consensus False

-

  Consensus:

- **-bc**

  Minimum support to call bases           0

- **-bcNano**

  Altered indel calling for ONT data      False

- **-bcd**

  Minimum depth to cal bases              1

- **-bcg**

  Maintain insignificant gaps             False

- **-ID**

  Minimum consensus ID                    1.0%

- **-dense**

  Skip insertion in consensus             False

- **-ref\_fsa**

  Use n's on indels                       False

-

  General:

- **-t\_db**

  Template DB

- **-p**

  P-value                                 0.05

- **-shm**

  Use DB in shared memory                 0

- **-mmap**

  Memory map \*.comp.b                     False

- **-tmp**

  Set directory for temporary files

- **-t**

  Number of threads                       1

- **-status**

  Extra status                            False

- **-verbose**

  Extra verbose                           False

- **-c**

  Citation

- **-v**

  Version

- **-h**

  Shows this help message

-

  Template mapping:

- **-ConClave**

  ConClave version                        1

- **-mem\_mode**

  Base ConClave on template mappings      False

- **-proxi**

  Proximity scoring (negative for soft)   False/1.0

- **-ex\_mode**

  Searh kmers exhaustively                False

- **-deCon**

  Remove contamination                    False

- **-Sparse**

  Only count kmers                        False

- **-ss**

  Sparse sorting (q,c,d)                  q

- **-Mt1**

  Map everything to one template          False/0

- **-pm**

  Pairing method (p,u,f)                  u

- **-1t1**

  One query to one template               False

- **-hmm**

  Use a HMM to assign template(s)         True

- **-ck**

  Count k-mers over pseudo alignment      False

-

  Chaining:

- **-k**

  K-mersize                               DB defined

- **-ts**

  Trim front of seeds                     0

- **-ssa**

  Seeds soround alignments                False

- **-ex\_mode**

  Searh kmers exhaustively                False

- **-fpm**

  Pairing method (p,u,f)                  u

- **-mq**

  Minimum mapping quality                 0

-

  Alignment:

- **-ca**

  Circular alignments                     False

- **-mrs**

  Minimum relative alignment score        0.5

- **-mrc**

  Minimum query coverage                  0.0

- **-ml**

  Minimum alignment length                16

- **-reward**

  Score for match                         1

- **-penalty**

  Penalty for mismatch                    2

- **-gapopen**

  Penalty for gap opening                 3

- **-gapextend**

  Penalty for gap extension               1

- **-per**

  Reward for pairing reads                7

- **-Npenalty**

  Penalty matching N                      0

- **-transition**

  Penalty for transition                  2

- **-transversion**

  Penalty for transversion                2

- **-sasm**

  Skip alignment                          False

-

  Trimming:

- **-mp**

  Minimum phred score                     20

- **-eq**

  Minimum avg. quality score              0

- **-5p**

  Trim 5 prime                            0

- **-3p**

  Trim 3 prime                            0

- **-ml**

  Minimum length                          16

- **-xl**

  Maximum length on se                    2147483647

- **-boot**

  Bootstrap sub-sequence                  False

-

  Presets:

- **-apm**

  Sets both pm and fpm                    u

- **-cge**

  Set CGE penalties and rewards           False

- **-mint2**

  Set 2ng gen Mintyper preset             False

- **-mint3**

  Set 3rd gen Mintyper preset             False

## AUTHOR

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