GT-TALLYMER-MKINDE(1)

NAME
gt-tallymer-mkindex - Count and index k-mers in the given enhanced suffix array for a fixed value of k.

SYNOPSIS

gt tallymer mkindex [options] -esa suffixerator-index [options]

OPTIONS

-esa
    specify suffixerator-index (mandatory option) (default: undefined)

-mersize
    Specify the mer size. (default: 20)

-minocc
    Specify the minimum occurrence number for the mers to output/index (default: 0)

-maxocc
    Specify the maximum occurrence number for the mers to output/index (default: 0)

-pl
    specify prefix length for bucket boundary construction recommendation: use without argument; then a reasonable prefix length is automatically determined (default: 0)

-indexname
    store the mers specified by options -maxocc and -minocc in an index (default: undefined)

-counts
    store counts of the mers (default: no)

-scan
    read enhanced suffix array sequentially instead of mapping it to memory (default: no)

-v
    be verbose (default: no)

-help
    display help and exit

-version
    display version information and exit

AUTHOR

Report bugs to <kurtz@zbh.uni-hamburg.de>.