Provided by: kma_1.4.14-2_amd64 
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.
kma 1.3.23 July 2021 KMA(1)