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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)
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--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)
Perform most operations on disk rather than in RAM (will slow down build in most cases)
September 2015 kraken-build 0.10.5~beta