kraken-build(1) 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)