# Install kraken2 with Homebrew, apt, apk Taxonomic sequence classification system. Version 2.17.1 via Homebrew; verified from local package data. Also installable with debian: sudo apt install kraken2. ## Install ```sh sudo av install brew:kraken2 ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install kraken2 ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install kraken2 ``` Evidence: Debian stable package indexes: kraken2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - apk (92%): ```sh sudo apk add k2 ``` Evidence: Alpine Linux edge package indexes: k2 from https://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz ## Package facts - **Package key:** brew:kraken2 - **Package manager:** Homebrew - **Version:** 2.17.1 - **Source summary:** Taxonomic sequence classification system - **Homepage:** - **Repository:** - **Generated:** 2026-08-03T19:37:03+00:00 ## Executables - k2 (alias) - kraken2 (alias) - kraken2-build (alias) - kraken2-inspect (alias) ## Install behavior - Bottle: not available ## Freshness - Page generated: 2026-08-03 - Package-manager version: 2.17.1 ## Project history and usage Kraken 2 is the second-generation Kraken taxonomic sequence classifier for DNA reads. It matters in bioinformatics packaging because it packages a high-performance, database-heavy scientific CLI into standard Unix package-manager workflows while still reflecting the research tool's unusually large external data requirements. ### Project history The original Kraken classifier was published in Genome Biology in 2014 as an ultrafast metagenomic sequence classification method based on exact k-mer alignments. Kraken 2 was created after Kraken 1's speed exposed a practical problem: large k-mer/LCA databases could demand enough RAM to make the tool hard to run on ordinary workstations. Kraken 2's manual describes the key redesign: it stores minimizers instead of every k-mer, uses a probabilistic compact hash table, supports translated search against amino-acid databases, and adds spaced seeds and special database support. The Kraken 2 paper was published in Genome Biology on 2019-11-28 and reported lower memory use and faster classification while keeping Kraken-style exact-match taxonomy assignment. ### Adoption history Kraken 2 became part of the common metagenomics command-line toolkit because it preserved Kraken's CLI-centered workflow while reducing the memory barrier for large microbial reference databases. Its Homebrew, Debian, Ubuntu, Alpine, and source-build packaging reflects the way sequencing labs and HPC users install reproducible command-line tools across mixed Linux and macOS environments. The project also kept compatibility with the surrounding Kraken ecosystem, including the original Kraken paper lineage and related abundance-estimation workflows such as Bracken, which helped make Kraken 2 an upgrade path rather than a disconnected replacement. ### How it is used Users install the program, then build or download a taxonomy database before classifying reads with commands such as kraken2, kraken2-build, and kraken2-inspect. The manual emphasizes that database construction depends on external taxonomy and sequence downloads, disk space, RAM, OpenMP-capable builds, and Unix utilities. For package managers, Kraken 2 is an example where the packaged executable is only part of the operational story: the large mutable reference database, network downloads, and local storage policy matter as much as the binary. ### Why package nerds care Kraken 2 is a package-nerd case study in scientific software distribution: a small CLI package fronts a large and evolving data dependency that cannot simply be vendored into the formula. It also shows why bioinformatics packages often need both upstream manuals and package-manager metadata to communicate runtime expectations. ### Timeline - 2014: The original Kraken paper was published in Genome Biology. - 2018-06-26: The Kraken 2 GitHub repository and v2.0.6-beta release were published. - 2019-11-28: The Kraken 2 paper was published in Genome Biology. - 2025-11-24: Kraken 2 v2.17.1 was published on GitHub. ### Related projects - Kraken 1 is the direct predecessor. Bracken is a related abundance-estimation tool commonly used with Kraken classification output. The broader method family includes other metagenomic classifiers and low-memory variants that respond to the same taxonomy-indexing tradeoffs. ### Sources - - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Other Package-Manager Records - Debian apt - kraken2 - 2.1.3-1: normalized package name match | Debian stable package indexes: kraken2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | taxonomic classification system using exact k-mer matches | https://www.ccb.jhu.edu/software/kraken2/ - Ubuntu apt - kraken2 - 2.1.3-1: normalized package name match | Ubuntu 24.04 LTS package indexes: kraken2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | taxonomic classification system using exact k-mer matches | https://www.ccb.jhu.edu/software/kraken2/ - apk - k2 - 0_git20260430-r0: installed executable or alias match | Alpine Linux edge package indexes: k2 from https://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz | Chess engine with UCI and Xboard interface | https://github.com/serg-meus/k2 ## Combined YAML source View the package source record on GitHub. [combined/kraken2.yml](https://github.com/mxcl/pkgdb/blob/main/combined/kraken2.yml) ## Sources - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph