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.

kma 1.1.7                                         February 2019                                           KMA(1)