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kraken-build - assigning taxonomic labels to short DNA sequences


kraken-build [task option] [options]


Task options (exactly one must be selected):
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

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

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

Remove unneeded files from a built database

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

Download and create default database

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

--help Print this message

Print version information


--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

--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)

Perform most operations on disk rather than in RAM (will slow down build in most

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