---
name: "gt-tallymer-mkindex"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-tallymer-mkindex"
---

# gt-tallymer-mkindex(1)

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

## 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\>.