NAME

       kraken-build - assigning taxonomic labels to short DNA sequences

SYNOPSIS

       kraken-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 "bacteria", "plasmids", "viruses", "human")

       --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)

       --rebuild
              Create DB from library like --build, but remove existing non-library/taxonomy files
              before build

       --clean
              Remove unneeded files from a built database

       --shrink NEW_CT
              Shrink an existing DB to have only NEW_CT k-mers

       --standard
              Download and create default database

       --upgrade
              Upgrade an existing older database to use scrambled minimizer ordering (see  README
              for details)

       --help Print this message

       --version
              Print version information

OPTIONS

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

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

       --new-db NAME
              New Kraken DB name (shrink task only; mandatory for shrink task)

       --kmer-len NUM
              K-mer length in bp (build/shrink tasks only; def: 31)

       --minimizer-len NUM
              Minimizer length in bp (build/shrink tasks only; def: 15)

       --jellyfish-hash-size STR
              Pass  a specific hash size argument to jellyfish when building database (build task
              only)

       --max-db-size SIZE
              Shrink the DB before full build, making sure database and  index  together  use  <=
              SIZE gigabytes (build task only)

       --shrink-block-offset NUM
              When  shrinking,  select the k-mer that is NUM positions from the end of a block of
              k-mers (default: 1)

       --work-on-disk
              Perform most operations on disk rather than in RAM (will slow down  build  in  most
              cases)