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>.