Provided by: kma_1.4.3-1_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.