This is the command gt-tallymer-mkindex that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 <[email protected]>.
Use gt-tallymer-mkindex online using onworks.net services
