kraken-build1
Assigning taxonomic labels to short dna sequences
Usage
kraken-build [task
option]
[options]
Overview
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)