Install kraken2 with Homebrew, apt, apk

Project links

• Homepage
• Upstream docs
• Package manager page

Commands and aliases

• k2
• kraken2
• kraken2-build
• kraken2-inspect

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

• https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46
• https://github.com/DerrickWood/kraken2
• https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown
• https://github.com/DerrickWood/kraken2/releases/tag/v2.0.6-beta
• https://github.com/DerrickWood/kraken2/releases/tag/v2.17.1
• https://link.springer.com/article/10.1186/s13059-019-1891-0