kma - maps and/or aligns raw reads to a template database

       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)

              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

       kma - maps and/or aligns raw reads to a template database