NAME

       kraken2-build - assigning taxonomic labels to short DNA sequences

SYNOPSIS

       kraken2-build [task option] [options]

DESCRIPTION

   Task options (exactly one must be selected):
       --download-taxonomy
              Download NCBI taxonomic information

       --download-library TYPE
              Download  partial  library  (TYPE  =  one  of  "archaea", "bacteria", "plasmid", "viral", "human",
              "fungi", "plant", "protozoa", "nr", "nt", "env_nr", "env_nt", "UniVec", "UniVec_Core")

       --special TYPE
              Download and build a special database (TYPE = one of "greengenes", "silva", "rdp")

       --add-to-library FILE
              Add FILE to library

       --build
              Create DB from library (requires taxonomy d/l'ed and at least one file in library)

       --clean
              Remove unneeded files from a built database

       --standard
              Download and build default database

       --help Print this message

       --version
              Print version information

OPTIONS

       --db NAME
              Kraken 2 DB/library name (mandatory except for --help/--version)

       --threads #
              Number of threads (def: 1)

       --kmer-len NUM
              K-mer length in bp/aa (build task only; def: 35 nt, 15 aa)

       --minimizer-len NUM
              Minimizer length in bp/aa (build task only; def: 31 nt, 15 aa)

       --minimizer-spaces NUM
              Number of characters in minimizer that are ignored in comparisons (build task only; def: 6  nt,  0
              aa)

       --protein
              Build a protein database for translated search

       --no-masking
              Used   with   --standard/--download-library/  --add-to-library  to  avoid  masking  low-complexity
              sequences prior to building; masking requires dustmasker or segmasker to  be  installed  in  PATH,
              which some users might not have.

       --max-db-size NUM
              Maximum  number  of bytes for Kraken 2 hash table; if the estimator determines more would normally
              be   needed,   the   reference   library   will   be    downsampled    to    fit.    (Used    with
              --build/--standard/--special)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

kraken2-build 2.0.7~beta                           March 2019                                   KRAKEN2-BUILD(1)