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

# kraken2(1)

assigning taxonomic labels to short DNA sequences

## NAME

kraken2 - assigning taxonomic labels to short DNA sequences

## SYNOPSIS

**kraken2** \[*options*\] *\<filename(s)\>*

## OPTIONS

- **--db** NAME

  Name for Kraken 2 DB (default: none)

- **--threads** NUM

  Number of threads (default: 1)

- **--quick**

  Quick operation (use first hit or hits)

- **--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

- **--confidence** FLOAT

  Confidence score threshold (default: 0.0); must be in \[0, 1\].

- **--minimum-base-quality** NUM

  Minimum base quality used in classification (def: 0, only effective with FASTQ input).

- **--report** FILENAME

  Print a report with aggregrate counts/clade to file

- **--use-mpa-style**

  With **--report**, format report output like Kraken 1's kraken-mpa-report

- **--report-zero-counts**

  With **--report**, report counts for ALL taxa, even if counts are zero

- **--memory-mapping**

  Avoids loading database into RAM

- **--paired**

  The filenames provided have paired-end reads

- **--use-names**

  Print scientific names instead of just taxids

- **--gzip-compressed**

  Input files are compressed with gzip

- **--bzip2-compressed**

  Input files are compressed with bzip2

- **--help**

  Print this message

- **--version**

  Print version information

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

## AUTHOR

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