# Install kallisto with Homebrew, apt, Nix Quantify abundances of transcripts from RNA-Seq data. Version 0.52.0 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:kallisto ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install kallisto ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install kallisto ``` Evidence: Debian stable package indexes: kallisto from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#kallisto ``` Evidence: nixpkgs package indexes: pkgs/by-name/ka/kallisto/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:kallisto - **Package manager:** Homebrew - **Package manager page:** - **Version:** 0.52.0 - **Source summary:** Quantify abundances of transcripts from RNA-Seq data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** BSD-2-Clause - **Source archive:** - **Generated:** 2026-07-08T18:08:21+00:00 ## Executables - kallisto (cli) - kallisto (alias) ## Dependencies - hdf5 ## Build dependencies - cmake ## 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: 0.52.0 - Local data: ok - Upstream repository: https://github.com/pachterlab/kallisto - Upstream latest detected: v0.52.0 (current) - info: No package-manager update timestamp was available. ## Project history and usage kallisto is a bioinformatics command-line program for quantifying transcript abundances from RNA-seq and related high-throughput sequencing data. Its significance comes from pseudoalignment: a faster compatibility test between reads and targets that avoids full alignment while retaining the information needed for quantification. ### Project history The public GitHub repository was created on 2014-11-13, and GitHub releases show v0.42 labeled as the first release on 2015-05-06. The 2016 Nature Biotechnology paper by Bray, Pimentel, Melsted, and Pachter introduced kallisto as a near-optimal probabilistic RNA-seq quantification program and described it as much faster than earlier approaches. The README and manual place the tool in a reproducible scientific workflow: build an index from a transcriptome, run quantification on paired-end or single-end reads, optionally bootstrap estimates, and analyze bulk RNA-seq output with sleuth. The repository also points to scripts for reproducing the paper results, reinforcing its role as both software and a published method. Later development extended kallisto's neighborhood beyond bulk RNA-seq. The README links kallisto with bustools and the kallisto-bustools ecosystem for preprocessing single-cell RNA-seq data, and releases in the 0.50.x and 0.51.x era reference long-read kallisto work before v0.52.0 restored genomebam and pseudobam functionality in 2026. ### Adoption history kallisto became widely packaged because it occupies a high-value scientific niche: a single executable that made transcript quantification fast enough for routine laptop and cluster workflows. The batch metadata lists Homebrew, Debian, Ubuntu, and Nix packages, while upstream releases provide binaries and source for research environments that pin methods by version. Its adoption is also tied to downstream method ecosystems. sleuth gave users a statistical analysis path for kallisto-quantified bulk RNA-seq, while bustools and kallisto-bustools made the pseudoalignment idea part of single-cell preprocessing workflows. ### How it is used A typical kallisto workflow builds a transcriptome index and then runs `kallisto quant` on sequencing reads to produce abundance estimates. The manual documents related commands such as `index`, `quant`, `bus`, `pseudo`, `merge`, and `h5dump`, making the package useful both for direct quantification and for integration into larger pipelines. Because kallisto is method software as much as a utility, users often cite the paper, pin the executable version, and keep index-building inputs alongside analysis scripts. ### Why package nerds care kallisto is a classic example of research software crossing into general package managers: it is small enough to install like a normal CLI, but scientifically important enough that packaging, versioning, and binary reproducibility matter. For package indexes, it also demonstrates the challenge of scientific CLI metadata: the package name is simple, but the real provenance includes a paper, a lab website, release binaries, and companion tools such as sleuth and bustools. ### Timeline - 2014: pachterlab/kallisto repository created. - 2015: v0.42 first release published on GitHub. - 2016: Near-optimal probabilistic RNA-seq quantification paper published in Nature Biotechnology. - 2024: v0.51.0 release named lr-kallisto. - 2026: v0.52.0 release restored genomebam and pseudobam features. ### Related projects - sleuth is the companion analysis project for kallisto-quantified bulk RNA-seq output. - bustools and kallisto-bustools extend the kallisto ecosystem into single-cell RNA-seq preprocessing. - The kallisto paper analysis repository contains scripts for reproducing the published results. ### 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:** kallisto - **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 - kallisto - 0.48.0+dfsg-4+b1: normalized package name match | Debian stable package indexes: kallisto from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | near-optimal RNA-Seq quantification | https://pachterlab.github.io/kallisto - Debian apt - kallisto-examples - 0.48.0+dfsg-4: normalized package name match | Debian stable package indexes: kallisto-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | near-optimal RNA-Seq quantification (example data) | https://pachterlab.github.io/kallisto - Nix - kallisto: normalized package name match | nixpkgs package indexes: pkgs/by-name/ka/kallisto/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - kallisto - 0.48.0+dfsg-4build1: normalized package name match | Ubuntu 24.04 LTS package indexes: kallisto from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | near-optimal RNA-Seq quantification | https://pachterlab.github.io/kallisto - Ubuntu apt - kallisto-examples - 0.48.0+dfsg-4build1: normalized package name match | Ubuntu 24.04 LTS package indexes: kallisto-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | near-optimal RNA-Seq quantification (example data) | https://pachterlab.github.io/kallisto ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [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. - [Database and data packages](https://www.automicvault.com/pkg/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [hdf5](https://www.automicvault.com/pkg/brew/hdf5/) - Runtime dependency declared by Homebrew. - [cmake](https://www.automicvault.com/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [stringtie](https://www.automicvault.com/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, quantification, rna-seq, 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. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [btllib](https://www.automicvault.com/pkg/brew/btllib/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [cutadapt](https://www.automicvault.com/pkg/brew/cutadapt/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastp](https://www.automicvault.com/pkg/brew/fastp/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [oarfish](https://www.automicvault.com/pkg/brew/oarfish/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, quantification, rna, rna-seq. - [rna-star](https://www.automicvault.com/pkg/brew/rna-star/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, rna, rna-seq, science. ## Combined YAML source View the package source record on GitHub. [combined/kallisto.yml](https://github.com/automic-vault/db/blob/main/combined/kallisto.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