SYNOPSIS

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)