# Install bowtie2 with Homebrew, apt, dnf, MacPorts, Nix, zypper Fast and sensitive gapped read aligner. Version 2.5.5 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:bowtie2 ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install bowtie2 ``` Evidence: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install bowtie2 ``` Evidence: MacPorts ports tree: science/bowtie2/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install bowtie2 ``` Evidence: Debian stable package indexes: bowtie2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install bowtie2 ``` Evidence: Fedora Rawhide package metadata: bowtie2 from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#bowtie2 ``` Evidence: nixpkgs package indexes: pkgs/by-name/bo/bowtie2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - zypper (92%): ```sh sudo zypper install bowtie2 ``` Evidence: openSUSE Tumbleweed package metadata: bowtie2 from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst ## Package facts - **Package key:** brew:bowtie2 - **Package manager:** Homebrew - **Package manager page:** - **Version:** 2.5.5 - **Source summary:** Fast and sensitive gapped read aligner - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** GPL-3.0-or-later - **Source archive:** - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - bowtie2 (cli) - bowtie2-align-l (cli) - bowtie2-align-s (cli) - bowtie2-build (cli) - bowtie2-build-l (cli) - bowtie2-build-s (cli) - bowtie2-inspect (cli) - bowtie2-inspect-l (cli) - bowtie2-inspect-s (cli) - bowtie2 (alias) - bowtie2-align-l (alias) - bowtie2-align-s (alias) - bowtie2-build (alias) - bowtie2-build-l (alias) - bowtie2-build-s (alias) - bowtie2-inspect (alias) - bowtie2-inspect-l (alias) - bowtie2-inspect-s (alias) ## Build dependencies - simde ## Uses from macOS - perl - python ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 2.5.5 - Local data: ok - Upstream repository: https://github.com/BenLangmead/bowtie2 - Upstream latest detected: v2.5.5 (current) - info: No package-manager update timestamp was available. ## Project history and usage Bowtie 2 is a fast, memory-efficient DNA sequencing read aligner and one of the canonical command-line tools in genomics packaging. It aligns sequencing reads to long reference genomes and emits SAM for downstream tools. ### Project history Bowtie 2 followed Bowtie 1, which the manual says was released in 2009 for the shorter reads common at the time. Bowtie 2 was introduced for longer reads and newer sequencing workloads, adding gapped alignment, local alignment, flexible paired-end handling, richer mapping qualities, and a different command-line and index format. The Bowtie 2 news archive shows beta releases in 2011. The main Bowtie 2 paper, 'Fast gapped-read alignment with Bowtie 2,' appeared in Nature Methods in 2012. The public GitHub repository was created in December 2012, and the official news archive notes that the source moved to GitHub in February 2014. ### Adoption history Bowtie 2 became a standard first-stage aligner for short-read sequencing pipelines, including variation calling, ChIP-seq, RNA-seq, bisulfite sequencing, and comparative genomics. The manual explicitly names SAMtools and GATK as downstream SAM consumers and says Bowtie 2 is tightly integrated into many other tools. Distribution is broad: the supplied package facts list Homebrew, Debian, Ubuntu, Fedora, MacPorts, Nix, and openSUSE, while the official manual highlights Bioconda and SourceForge binaries. Prebuilt genome indexes on the official site further cement it as a practical packaged tool rather than just a paper artifact. ### How it is used Users build or download a Bowtie 2 index for a reference genome, run `bowtie2` against FASTQ reads, and feed SAM output into downstream genomics tools. Companion commands include `bowtie2-build` for index construction and `bowtie2-inspect` for index inspection. Bowtie 2 is optimized for typical Illumina-style reads aligned to long genomes, while still handling local, end-to-end, paired-end, and very long read cases with different performance tradeoffs. ### Why package nerds care Bowtie 2 is significant because it is both research software and production infrastructure. Package maintainers care about CPU threading, index formats, bundled or external compression libraries, reproducible versions for scientific workflows, and compatibility with SAM/BAM pipelines. It is also a good example of bioinformatics packaging culture: official SourceForge releases, GitHub development, Bioconda-first scientific distribution, system packages, downloadable reference indexes, and citation-driven adoption all coexist. ### Timeline - 2009: Bowtie 1 released for then-common short sequencing reads. - 2011: Bowtie 2 beta releases appeared in the official news archive. - 2012: Bowtie 2 paper published in Nature Methods. - 2012: Public GitHub repository created. - 2014: Official news archive announced Bowtie 2 source on GitHub. - 2018: Thread-scaling paper published for high-thread-count processors. - 2026: Bowtie 2 v2.5.5 listed as the latest official release. ### Related projects - Bowtie 1 is the predecessor for shorter, ungapped alignments. - SAMtools and GATK are downstream tools named by the manual as SAM consumers. - BWA, minimap2, STAR, and HISAT2 are related read aligners in genomics workflows. - Bioconda is a major distribution channel for scientific command-line packages including Bowtie 2. ### Sources - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bowtie2 - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - bowtie2 - 2.5.4-1+b2: normalized package name match | Debian stable package indexes: bowtie2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | ultrafast memory-efficient short read aligner | https://bowtie-bio.sourceforge.net/bowtie2 - Debian apt - bowtie2-examples - 2.5.4-1: normalized package name match | Debian stable package indexes: bowtie2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Examples for bowtie2 | https://bowtie-bio.sourceforge.net/bowtie2 - Nix - bowtie2: normalized package name match | nixpkgs package indexes: pkgs/by-name/bo/bowtie2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bowtie2 - 2.5.2-1: normalized package name match | Ubuntu 24.04 LTS package indexes: bowtie2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | ultrafast memory-efficient short read aligner | https://bowtie-bio.sourceforge.net/bowtie2 - Ubuntu apt - bowtie2-examples - 2.5.2-1: normalized package name match | Ubuntu 24.04 LTS package indexes: bowtie2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Examples for bowtie2 | https://bowtie-bio.sourceforge.net/bowtie2 - dnf - bowtie2 - 2.5.4-1.fc45: normalized package name match | Fedora Rawhide package metadata: bowtie2 from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | An ultra fast and memory-efficient read aligner | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - zypper - bowtie2 - 2.5.4-2.4: normalized package name match | openSUSE Tumbleweed package metadata: bowtie2 from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst | Fast and memory-efficient short read aligner | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - MacPorts - bowtie2: normalized package name match | MacPorts ports tree: science/bowtie2/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Related links - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://www.automicvault.com/pkg/brew-utility-packages/) - Matched Homebrew package provider. - [breseq](https://www.automicvault.com/pkg/brew/breseq/) - Popular package that depends on this formula. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [fgbio](https://www.automicvault.com/pkg/brew/fgbio/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [htslib](https://www.automicvault.com/pkg/brew/htslib/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [sambamba](https://www.automicvault.com/pkg/brew/sambamba/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [samtools](https://www.automicvault.com/pkg/brew/samtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. ## Combined YAML source View the package source record on GitHub. [combined/bowtie2.yml](https://github.com/automic-vault/db/blob/main/combined/bowtie2.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph