.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH KMA "1" "July 2021" "kma 1.3.23" "User Commands"
.SH NAME
kma \- maps and/or aligns raw reads to a template database
.SH DESCRIPTION
.IP
KMA\-1.3.23 maps and/or aligns raw reads to a template database.
.TP
Options:
Desc:                                   Default:
.IP
Input:
.TP
\fB\-i\fR
Single end input(s)                     stdin
.TP
\fB\-ipe\fR
Paired end input(s)                     
.TP
\fB\-int\fR
Interleaved input(s)                    
.IP
Output:
.TP
\fB\-o\fR
Output prefix                           
.TP
\fB\-ef\fR
Output additional features              False
.TP
\fB\-vcf\fR
Output vcf file, 2 to apply FT          False
.TP
\fB\-sam\fR
Output sam, 4/2096 for mapped/aligned   False
.TP
\fB\-nc\fR
No consensus file                       False
.TP
\fB\-nc\fR
No aln file                             False
.TP
\fB\-nf\fR
No frag file                            False
.TP
\fB\-matrix\fR
Output assembly matrix                  False
.TP
\fB\-a\fR
Output all template mappings            False
.TP
\fB\-and\fR
Use both mrs and p\-value on consensus   or
.TP
\fB\-oa\fR
Use neither mrs or p\-value on consensus False
.IP
Consensus:
.TP
\fB\-bc\fR
Minimum support to call bases           0
.TP
\fB\-bcNano\fR
Altered indel calling for ONT data      False
.TP
\fB\-bcd\fR
Minimum depth to cal bases              1
.TP
\fB\-bcg\fR
Maintain insignificant gaps             False
.TP
\fB\-ID\fR
Minimum consensus ID                    1.0%
.TP
\fB\-dense\fR
Skip insertion in consensus             False
.TP
\fB\-ref_fsa\fR
Use n's on indels                       False
.IP
General:
.TP
\fB\-t_db\fR
Template DB                             
.TP
\fB\-p\fR
P\-value                                 0.05
.TP
\fB\-shm\fR
Use DB in shared memory                 0
.TP
\fB\-mmap\fR
Memory map *.comp.b                     False
.TP
\fB\-tmp\fR
Set directory for temporary files       
.TP
\fB\-t\fR
Number of threads                       1
.TP
\fB\-status\fR
Extra status                            False
.TP
\fB\-verbose\fR
Extra verbose                           False
.TP
\fB\-c\fR
Citation                                
.TP
\fB\-v\fR
Version                                 
.TP
\fB\-h\fR
Shows this help message                 
.IP
Template mapping:
.TP
\fB\-ConClave\fR
ConClave version                        1
.TP
\fB\-mem_mode\fR
Base ConClave on template mappings      False
.TP
\fB\-proxi\fR
Proximity scoring (negative for soft)   False/1.0
.TP
\fB\-ex_mode\fR
Searh kmers exhaustively                False
.TP
\fB\-deCon\fR
Remove contamination                    False
.TP
\fB\-Sparse\fR
Only count kmers                        False
.TP
\fB\-ss\fR
Sparse sorting (q,c,d)                  q
.TP
\fB\-Mt1\fR
Map everything to one template          False/0
.TP
\fB\-pm\fR
Pairing method (p,u,f)                  u
.TP
\fB\-1t1\fR
One query to one template               False
.TP
\fB\-hmm\fR
Use a HMM to assign template(s)         True
.TP
\fB\-ck\fR
Count k\-mers over pseudo alignment      False
.IP
Chaining:
.TP
\fB\-k\fR
K\-mersize                               DB defined
.TP
\fB\-ts\fR
Trim front of seeds                     0
.TP
\fB\-ssa\fR
Seeds soround alignments                False
.TP
\fB\-ex_mode\fR
Searh kmers exhaustively                False
.TP
\fB\-fpm\fR
Pairing method (p,u,f)                  u
.TP
\fB\-mq\fR
Minimum mapping quality                 0
.IP
Alignment:
.TP
\fB\-ca\fR
Circular alignments                     False
.TP
\fB\-mrs\fR
Minimum relative alignment score        0.5
.TP
\fB\-mrc\fR
Minimum query coverage                  0.0
.TP
\fB\-ml\fR
Minimum alignment length                16
.TP
\fB\-reward\fR
Score for match                         1
.TP
\fB\-penalty\fR
Penalty for mismatch                    2
.TP
\fB\-gapopen\fR
Penalty for gap opening                 3
.TP
\fB\-gapextend\fR
Penalty for gap extension               1
.TP
\fB\-per\fR
Reward for pairing reads                7
.TP
\fB\-Npenalty\fR
Penalty matching N                      0
.TP
\fB\-transition\fR
Penalty for transition                  2
.TP
\fB\-transversion\fR
Penalty for transversion                2
.TP
\fB\-sasm\fR
Skip alignment                          False
.IP
Trimming:
.TP
\fB\-mp\fR
Minimum phred score                     20
.TP
\fB\-eq\fR
Minimum avg. quality score              0
.TP
\fB\-5p\fR
Trim 5 prime                            0
.TP
\fB\-3p\fR
Trim 3 prime                            0
.TP
\fB\-ml\fR
Minimum length                          16
.TP
\fB\-xl\fR
Maximum length on se                    2147483647
.TP
\fB\-boot\fR
Bootstrap sub\-sequence                  False
.IP
Presets:
.TP
\fB\-apm\fR
Sets both pm and fpm                    u
.TP
\fB\-cge\fR
Set CGE penalties and rewards           False
.TP
\fB\-mint2\fR
Set 2ng gen Mintyper preset             False
.TP
\fB\-mint3\fR
Set 3rd gen Mintyper preset             False
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.