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)