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>.