table of contents
| KRAKEN2-BUILD(1) | User Commands | KRAKEN2-BUILD(1) |
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.
| March 2019 | kraken2-build 2.0.7~beta |