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KMA(1) User Commands KMA(1)

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.
Desc: Default:
Input:
Single end input(s) stdin
Paired end input(s)
Interleaved input(s)
Output:
Output prefix
Output additional features False
Output vcf file, 2 to apply FT False
Output sam, 4/2096 for mapped/aligned False
No consensus file False
No aln file False
No frag file False
Output assembly matrix False
Output all template mappings False
Use both mrs and p-value on consensus or
Use neither mrs or p-value on consensus False
Consensus:
Minimum support to call bases 0
Altered indel calling for ONT data False
Minimum depth to cal bases 1
Maintain insignificant gaps False
Minimum consensus ID 1.0%
Skip insertion in consensus False
Use n's on indels False
General:
Template DB
P-value 0.05
Use DB in shared memory 0
Memory map *.comp.b False
Set directory for temporary files
Number of threads 1
Extra status False
Extra verbose False
Citation
Version
Shows this help message
Template mapping:
ConClave version 1
Base ConClave on template mappings False
Proximity scoring (negative for soft) False/1.0
Searh kmers exhaustively False
Remove contamination False
Only count kmers False
Sparse sorting (q,c,d) q
Map everything to one template False/0
Pairing method (p,u,f) u
-1t1
One query to one template False
Use a HMM to assign template(s) True
Count k-mers over pseudo alignment False
Chaining:
K-mersize DB defined
Trim front of seeds 0
Seeds soround alignments False
Searh kmers exhaustively False
Pairing method (p,u,f) u
Minimum mapping quality 0
Alignment:
Circular alignments False
Minimum relative alignment score 0.5
Minimum query coverage 0.0
Minimum alignment length 16
Score for match 1
Penalty for mismatch 2
Penalty for gap opening 3
Penalty for gap extension 1
Reward for pairing reads 7
Penalty matching N 0
Penalty for transition 2
Penalty for transversion 2
Skip alignment False
Trimming:
Minimum phred score 20
Minimum avg. quality score 0
-5p
Trim 5 prime 0
-3p
Trim 3 prime 0
Minimum length 16
Maximum length on se 2147483647
Bootstrap sub-sequence False
Presets:
Sets both pm and fpm u
Set CGE penalties and rewards False
Set 2ng gen Mintyper preset False
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.

July 2021 kma 1.3.23