superk

kmtricks superk

kmtricks superk allows to compute super-k-mers from a sample and dispatch them into partitions according to their minimizers. It can be run only after kmtricks repart or kmtricks pipeline --until repart. It takes a sample id (see inputs) and an optional list of partitions if you need to compute only specific partitions.

Usage

kmtricks superk v1.0.0

DESCRIPTION
  Compute super-k-mers.

USAGE
  kmtricks superk --run-dir <DIR> --id <STR> [--restrict-to-list <STR>] [-t/--threads <INT>] 
                  [-v/--verbose <STR>] [--cpr] [-h/--help] [--version] 

OPTIONS
  [global]
     --run-dir          - kmtricks runtime directory. 
     --id               - sample ID, as define in the input fof. 
     --restrict-to-list - process only some partitions, comma separated. 
     --cpr              - output compressed super-k-mers. [⚑]

  [common]
    -t --threads - number of threads. {8}
    -h --help    - show this message and exit. [⚑]
       --version - show version and exit. [⚑]
    -v --verbose - verbosity level [debug|info|warning|error]. {info}