KRAKEN2-BUILD

NAME

kraken2-build - assigning taxonomic labels to short DNA sequences

SYNOPSIS

kraken2-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 "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-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.

--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)

AUTHOR

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