count

kmtricks count

kmtricks count allows to count super-k-mers partitions of a sample. It can be run only after kmtricks superk or kmtricks pipeline --until superk.

• --mode kmer: output counted k-mers
• --mode kff: output counted k-mer in kff format (the next steps are not compatible with this format)
• --mode hash: output counted hashes
• --mode vector: output hashes as bit-vectors
• --partition-id: count specific partition (corresponding super-k-mer partition must have been computed before)

Usage

kmtricks count v1.0.0

DESCRIPTION
  Count k-mers/hashes in partitions.

USAGE
  kmtricks count --id <STR> --run-dir <DIR> --mode <STR> [--abundance-min <INT>] [--partition-id <INT>] 
                 [-t/--threads <INT>] [-v/--verbose <STR>] [--hist] [--clear] [--cpr] 
                 [-h/--help] [--version] 

OPTIONS
  [global]
     --id            - sample ID, as define in kmtricks fof. 
     --run-dir       - kmtricks runtime directory. 
     --abundance-min - min abundance to keep a k-mer/hash. {2}
     --partition-id  - partition id (default: all partitions are processed. {-1}
     --mode          - count k-mers or hashes. [kmer|hash|vector|kff] 
     --hist          - compute k-mer histograms. [⚑]
     --clear         - clear super-k-mer files. [⚑]
     --cpr           - output compressed partitions. [⚑]

  [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}