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]

DESCRIPTION

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

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

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

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

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

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

       -counts [yes|no]
           store counts of the mers (default: no)

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

       -v [yes|no]
           be verbose (default: no)

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

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

GenomeTools 1.6.1                                  02/09/2020                              GT-TALLYMER-MKINDE(1)