kraken2-build1
Assigning taxonomic labels to short dna sequences
Usage
kraken2-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 "archaea", "bacteria", "plasmid", "viral", "human", "fungi", "plant", "protozoa", "nr", "nt", "env_nr", "env_nt", "UniVec", "UniVec_Core")
-
--special TYPE -
Download and build a special database (TYPE = one of "greengenes", "silva", "rdp")
-
--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)
-
--clean -
Remove unneeded files from a built database
-
--standard -
Download and build default database
-
--help -
Print this message
-
--version -
Print version information
Options
-
--db NAME -
Kraken 2 DB/library name (mandatory except for
--help/--version)
-
--threads # -
Number of threads (def: 1)
-
--kmer-len NUM -
K-mer length in bp/aa (build task only; def: 35 nt, 15 aa)
-
--minimizer-len NUM -
Minimizer length in bp/aa (build task only; def: 31 nt, 15 aa)
-
--minimizer-spaces NUM -
Number of characters in minimizer that are ignored in comparisons (build task only; def: 6 nt, 0 aa)
-
--protein -
Build a protein database for translated search
-
--no-masking -
Used with
--standard/--download-library/--add-to-libraryto avoid masking low-complexity sequences prior to building; masking requires dustmasker or segmasker to be installed in PATH, which some users might not have.
-
--max-db-size NUM -
Maximum number of bytes for Kraken 2 hash table; if the estimator determines more would normally be needed, the reference library will be downsampled to fit. (Used with
--build/--standard/--special)
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).