---
name: "kraken2-build"
section: "1"
platform: "linux"
package: "kraken2"
version: "2.1.3-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kraken2-build"
---

# kraken2-build(1)

assigning taxonomic labels to short DNA sequences

## 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.