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.