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| KRAKEN-BUILD(1) |
User Commands |
KRAKEN-BUILD(1) |
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)
