NAME

       kma - mapps raw reads to a template database

DESCRIPTION

       mapps raw reads to a template database.

OPTIONS

       -o     Output file                     None            REQUIRED

       -t_db  Template DB                     None            REQUIRED

       -i     Input file name(s)              STDIN

       -ipe   Input paired end file name(s)

       -int   Input interleaved file name(s)

       -k     Kmersize                        DB defined

       -e     evalue                          0.05

       -ConClave
              ConClave version                1

       -mem_mode
              Use kmers to choose best template, and save memory       False

       -ex_mode
              Searh kmers exhaustively        False

       -ef    Print additional features       False

       -vcf   Make vcf file, 2 to apply FT    False/0

       -deCon Remove contamination            False

       -dense Do not allow insertions in assembly                     False

       -ref_fsa
              Consensus sequnce will have "n" instead of gaps        False

       -matrix
              Print assembly matrix           False

       -a     Print all best mappings         False

       -mp    Minimum phred score             30

       -5p    Cut a constant number of nucleotides from the 5 prime.   0

       -Sparse
              Only count kmers                False

       -Mt1   Map only to "num" template.     0 / False

       -ID    Minimum ID                      1.0%

       -ss    Sparse sorting (q,c,d)          q

       -pm    Pairing method (p,u,f)          u

       -fpm   Fine Pairing method (p,u,f)     u

       -apm   Sets both pm and fpm            u

       -shm   Use shared DB made by kma_shm   0 (lvl)

       -swap  Swap DB to disk                 0 (lvl)

       -1t1   Skip HMM                        False

       -ck    Count kmers instead of pseudo alignment                False

       -ca    Make circular alignments        False

       -boot  Bootstrap sequence              False

       -bc    Base calls should be significantly overrepresented.  [True]

       -bc90  Base  calls  should  be both significantly overrepresented, and have 90% agreement.
              False

       -bcNano
              Call bases at suspicious deletions, made for nanopore.   False

       -and   Both mrs and p_value thresholds has to reached to in order  to  report  a  template
              hit.          or

       -mq    Minimum mapping quality         0

       -mrs   Minimum alignment score, normalized to alignment length  0.50

       -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

       -cge   Set CGE penalties and rewards   False

       -t     Number of threads               1

       -v     Version

       -h     Shows this help message

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.