---
name: "kraken-build"
section: "1"
platform: "linux"
package: "kraken"
version: "1.1.1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kraken-build"
---

# kraken-build(1)

assigning taxonomic labels to short DNA sequences

## NAME

kraken-build - assigning taxonomic labels to short DNA sequences

## SYNOPSIS

**kraken-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 "bacteria", "plasmids", "viruses", "human")

- **--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)

- **--rebuild**

  Create DB from library like **--build**, but remove existing non-library/taxonomy files before build

- **--clean**

  Remove unneeded files from a built database

- **--shrink** NEW\_CT

  Shrink an existing DB to have only NEW\_CT k-mers

- **--standard**

  Download and create default database

- **--upgrade**

  Upgrade an existing older database to use scrambled minimizer ordering (see README for details)

- **--help**

  Print this message

- **--version**

  Print version information

## OPTIONS

- **--db** NAME

  Kraken DB/library name (mandatory except for **--help**/--version)

- **--threads** #

  Number of threads (def: 1)

- **--new-db** NAME

  New Kraken DB name (shrink task only; mandatory for shrink task)

- **--kmer-len** NUM

  K-mer length in bp (build/shrink tasks only; def: 31)

- **--minimizer-len** NUM

  Minimizer length in bp (build/shrink tasks only; def: 15)

- **--jellyfish-hash-size** STR

  Pass a specific hash size argument to jellyfish when building database (build task only)

- **--max-db-size** SIZE

  Shrink the DB before full build, making sure database and index together use \<= SIZE gigabytes (build task only)

- **--shrink-block-offset** NUM

  When shrinking, select the k-mer that is NUM positions from the end of a block of k-mers (default: 1)

- **--work-on-disk**

  Perform most operations on disk rather than in RAM (will slow down build in most cases)