# Install alevin-fry with Homebrew Efficient and flexible tool for processing single-cell sequencing data. Version 0.16.0 via Homebrew; verified 2026-07-08. ## Install ```sh sudo av install brew:alevin-fry ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install alevin-fry ``` Evidence: local Homebrew formula metadata ## Package facts - **Package key:** brew:alevin-fry - **Package manager:** Homebrew - **Package manager page:** - **Version:** 0.16.0 - **Source summary:** Efficient and flexible tool for processing single-cell sequencing data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** BSD-3-Clause - **Source archive:** - **Last updated:** 2026-07-08T03:19:30Z - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - alevin-fry (cli) - alevin-fry (alias) ## Build dependencies - cmake - rust ## Uses from macOS - bzip2 ## 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: 0.16.0 - Package-manager updated: 2026-07-08 - Local data: ok - Upstream repository: https://github.com/COMBINE-lab/alevin-fry - Upstream latest detected: v0.16.0 (current) ## Project history and usage alevin-fry is a Rust command-line suite for rapid, accurate, and memory-frugal processing of single-cell and single-nucleus sequencing data. It is a bioinformatics package where packaging matters because users often need reproducible pipelines more than interactive software. ### Project history The official README says alevin-fry consumes RAD files produced by piscem or salmon alevin, generates permit lists, and estimates distinct molecules per gene per cell. The project focuses on safety, accuracy, time efficiency, and memory efficiency. The README and documentation present alevin-fry as the successor to alevin. It subsumes core alevin features, adds capabilities, improves performance, and is where the maintainers expect most future method development to happen, while salmon alevin remains maintained for users not ready to migrate. The project was described in the 2022 Nature Methods paper 'Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data.' Its changelog shows active releases through the 0.9 series, including USA-mode support, UMI resolution modes, dependency updates, and command-line validation improvements. ### Adoption history The official README documents Bioconda availability for x86 Linux and macOS, crates.io installation through Cargo, and source builds with Cargo. The supplied package facts add Homebrew packaging, while the README points to Bioconda badges, tutorials, GitHub discussions, and downstream R/Bioconductor loading paths. The adoption story is workflow-oriented: alevin-fry is meant to sit in pipelines with piscem or salmon upstream and fishpond, alevinQC, pyroe, or SingleCellExperiment downstream. The project also recommends simpleaf as a wrapper/workflow runner to make common reference-building and quantification workflows easier. ### How it is used Users typically produce RAD files with piscem or salmon alevin, then use alevin-fry commands such as permit-list generation, collation, quantification, and inference. The Read the Docs site organizes this around commands including `generate-permit-list`, `collate`, `quant`, `infer`, and `atac`. Installation is intentionally package-manager friendly: `conda install -c bioconda alevin-fry`, `cargo install alevin-fry`, Homebrew packaging, or a direct source build with `cargo build --release`. ### Why package nerds care alevin-fry matters to package nerds because it is a scientific CLI whose real unit of use is the reproducible workflow. Versioned binaries, Bioconda, Cargo, Homebrew, and documentation all reduce friction for lab pipelines and HPC environments. It also shows the Rust-in-bioinformatics pattern: performance-sensitive command-line genomics tools distributed through both language-native crates and scientific package channels. ### Timeline - 2021-06-29: bioRxiv preprint posted for alevin-fry. - 2021-07-22: Changelog records 0.4.1 with metadata/output changes. - 2021-10-16: 0.4.2 added USA mode support to `infer`. - 2022-03-01: Nature Methods paper published. - 2022-06-01: 0.6.0 added UMI resolution and command-line validation work. - 2022-10-11: 0.8.0 fixed force-cells and expect-cells parsing. - 2024-03-08: 0.9.0 released with libradicl compatibility work. ### Related projects - The official README names piscem and salmon as RAD-file producers; simpleaf as a wrapper/workflow runner; pyroe for enhanced transcriptome construction; fishpond for R ingestion; and alevinQC for quality control. - The documentation also connects alevin-fry output to Bioconductor's SingleCellExperiment ecosystem. ### Sources - - - - - source_facts.package-manager ## Security Notes No matching local secret-handling manifest was found for alevin-fry. Nucleus package metadata is still published here so future coverage has a stable package URL. ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** alevin-fry - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 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. - [cmake](https://www.automicvault.com/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [rust](https://www.automicvault.com/pkg/brew/rust/) - Build dependency declared by Homebrew. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - 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. - [fastq-tools](https://www.automicvault.com/pkg/brew/fastq-tools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastqc](https://www.automicvault.com/pkg/brew/fastqc/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. ## Combined YAML source View the package source record on GitHub. [combined/alevin-fry.yml](https://github.com/automic-vault/db/blob/main/combined/alevin-fry.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 - cross-ecosystem install command graph