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kraken2-build - assigning taxonomic labels to short DNA sequences


kraken2-build [task option] [options]


Task options (exactly one must be selected):

Download NCBI taxonomic information
Download partial library (TYPE = one of "archaea", "bacteria", "plasmid", "viral", "human", "fungi", "plant", "protozoa", "nr", "nt", "env_nr", "env_nt", "UniVec", "UniVec_Core")
Download and build a special database (TYPE = one of "greengenes", "silva", "rdp")
Add FILE to library
Create DB from library (requires taxonomy d/l'ed and at least one file in library)
Remove unneeded files from a built database
Download and build default database
Print this message
Print version information


Kraken 2 DB/library name (mandatory except for --help/--version)
Number of threads (def: 1)
K-mer length in bp/aa (build task only; def: 35 nt, 15 aa)
Minimizer length in bp/aa (build task only; def: 31 nt, 15 aa)
Number of characters in minimizer that are ignored in comparisons (build task only; def: 6 nt, 0 aa)
Build a protein database for translated search
Used with --standard/--download-library/ --add-to-library to avoid masking low-complexity sequences prior to building; masking requires dustmasker or segmasker to be installed in PATH, which some users might not have.
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)


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

March 2019 kraken2-build 2.0.7~beta