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Téo Lemane edited this page Jul 29, 2021 · 2 revisions

kmtricks index allows to query an HowDeSBT's index built with kmtricks's Bloom filters. See examples.

Usage

kmtricks query v1.0.0

DESCRIPTION
  Query HowDeSBT index.

USAGE
  kmtricks query --run-dir <DIR> --query <FILE> [--output <FILE>] [--threshold <FLOAT>] [-t/--threads <INT>] 
                 [-v/--verbose <STR>] [--sort] [--consistency-check] [-h/--help] [--version] 

OPTIONS
  [global]
     --run-dir           - kmtricks runtime directory 
     --query             - query file (fasta/fastq/txt) 
     --output            - output file. {stdout}
     --threshold         - fraction of query kmers that must be present in a leaf to be considered a match {0.7}
     --sort              - sort matched leaves by the number of query kmers present [⚑]
     --consistency-check - check Bloom filter properties across the tree [⚑]

  [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}
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