kma1

Overview

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