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>.

                                                   10/07/2012                              GT-TALLYMER-MKINDE(1)