# 使用 Homebrew, apt, Nix 安装 kallisto 查看 kallisto 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:kallisto ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install kallisto ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install kallisto ``` 证据: 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 ``` 证据: nixpkgs package indexes: pkgs/by-name/ka/kallisto/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## 软件包事实 - **软件包键:** brew:kallisto - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 0.52.0 - **来源摘要:** Quantify abundances of transcripts from RNA-Seq data - **主页:** - **仓库:** - **上游文档:** - **许可证:** BSD-2-Clause - **源码归档:** - **已生成:** 2026-07-08T18:08:21+00:00 ## 可执行文件 - kallisto (cli) - kallisto (别名) ## 依赖 - hdf5 ## 构建依赖 - cmake ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-07-08 - 管理器版本: 0.52.0 - 本地数据: OK - 上游仓库: https://github.com/pachterlab/kallisto - 检测到的最新版本: v0.52.0 (当前) - 信息: No package-manager update timestamp was available. ## 项目历史与用法 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. ### 项目历史 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. ### 采用历史 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. ### 使用方式 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. ### 为什么软件包爱好者会关心 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. ### 时间线 - 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. ### 来源 - - - - - - - - ## 安全说明 narrow executable package without higher-risk signals. - **Geiger 风险:** 绿色 / 低 - narrow executable package without higher-risk signals ## 源数据库详情 - **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 ## 其他软件包管理器记录 - 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 ## 相关链接 - [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Database and data packages](https://www.automicvault.com/zh-hans/pkg/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [hdf5](https://www.automicvault.com/zh-hans/pkg/brew/hdf5/) - Runtime dependency declared by Homebrew. - [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [stringtie](https://www.automicvault.com/zh-hans/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, quantification, rna-seq, science. - [adapterremoval](https://www.automicvault.com/zh-hans/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [alevin-fry](https://www.automicvault.com/zh-hans/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bbtools](https://www.automicvault.com/zh-hans/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bowtie2](https://www.automicvault.com/zh-hans/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [btllib](https://www.automicvault.com/zh-hans/pkg/brew/btllib/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [cutadapt](https://www.automicvault.com/zh-hans/pkg/brew/cutadapt/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastp](https://www.automicvault.com/zh-hans/pkg/brew/fastp/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [oarfish](https://www.automicvault.com/zh-hans/pkg/brew/oarfish/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, quantification, rna, rna-seq. - [rna-star](https://www.automicvault.com/zh-hans/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) ## 来源 - 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