gt-tallymer-mkindex1
Count and index k-mers in the given enhanced suffix array for a fixed value of k.
Usage
gt tallymer
mkindex
[options]
-esa
suffixerator-index
[options]
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.