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

# kraken(1)

assigning taxonomic labels to short DNA sequences

## NAME

kraken - assigning taxonomic labels to short DNA sequences

## SYNOPSIS

**kraken** \[*options*\] *\<filename(s)\>*

## OPTIONS

- **--db** NAME

  Name for Kraken DB (default: none)

- **--threads** NUM

  Number of threads (default: 1)

- **--fasta-input**

  Input is FASTA format

- **--fastq-input**

  Input is FASTQ format

- **--gzip-compressed**

  Input is gzip compressed

- **--bzip2-compressed**

  Input is bzip2 compressed

- **--quick**

  Quick operation (use first hit or hits)

- **--min-hits** NUM

  In quick op., number of hits req'd for classification NOTE: this is ignored if **--quick** is not specified

- **--unclassified-out** FILENAME

  Print unclassified sequences to filename

- **--classified-out** FILENAME

  Print classified sequences to filename

- **--output** FILENAME

  Print output to filename (default: stdout); "-" will suppress normal output

- **--only-classified-output**

  Print no Kraken output for unclassified sequences

- **--preload**

  Loads DB into memory before classification

- **--paired**

  The two filenames provided are paired-end reads

- **--check-names**

  Ensure each pair of reads have names that agree with each other; ignored if **--paired** is not specified

- **--help**

  Print this message

- **--version**

  Print version information

If none of the \*-input or \*-compressed flags are specified, and the file is a regular file, automatic format detection is attempted.