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


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


-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:

-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)

display help and exit

display version information and exit


Report bugs to <[email protected]>.

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