# Install oarfish with Homebrew Long read RNA-seq quantification. Version 0.10.3 via Homebrew; verified 2026-07-27. ## Install ```sh sudo av install brew:oarfish ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install oarfish ``` Evidence: local Homebrew formula metadata ## Package facts - **Package key:** brew:oarfish - **Package manager:** Homebrew - **Version:** 0.10.3 - **Source summary:** Long read RNA-seq quantification - **Homepage:** - **Repository:** - **Last updated:** 2026-07-27T05:36:42Z - **Generated:** 2026-08-03T19:37:03+00:00 ## Executables - oarfish (alias) ## Install behavior - Bottle: not available ## Freshness - Page generated: 2026-08-03 - Package-manager version: 0.10.3 ## Project history and usage oarfish is a Rust tool from COMBINE-lab for transcript-level quantification from long-read RNA-seq data, including Oxford Nanopore cDNA/direct RNA and PacBio reads. It allocates multi-mapping reads probabilistically with an expectation-maximization model and adds coverage information to improve isoform-level estimates. ### Project history The GitHub repository was created on June 27, 2022. The project emerged from the COMBINE-lab lineage of RNA-seq quantification tools, applying probabilistic transcript-assignment ideas to long-read sequencing rather than short-read workflows. ### Adoption history The method was described in the 2024 preprint and later Bioinformatics paper "Enhanced probabilistic modeling leads to improved accuracy in long-read transcriptome quantification." Distribution through GitHub releases, Cargo, Bioconda, and Homebrew made it available to both Rust users and bioinformatics workflow environments. ### How it is used oarfish accepts transcriptome BAM alignments, raw reads that it maps internally, genome reads that are spliced-aligned and projected to transcripts, or existing genome BAMs projected against a transcript annotation. The common workflow is to supply long-read RNA-seq data plus transcript sequences or annotation, then produce transcript abundance estimates with optional bootstrap uncertainty and coverage modeling. ### Why package nerds care For package watchers, oarfish is a good example of scientific software moving through several distribution channels at once: a Rust codebase and Cargo package, prebuilt GitHub release binaries, Bioconda recipes for workflow managers, and a Homebrew formula for local command-line installs. ### Timeline - 2022-06-27: COMBINE-lab/oarfish repository was created. - 2024-02-28: The oarfish preprint was posted to bioRxiv. - 2026-06-07: GitHub release v0.10.0 was published. ### Related projects - The documentation compares or connects oarfish with NanoCount-style filters, minimap2 and other aligners for BAM input, rammap for in-process long-read mapping, and bramble for genome-to-transcript projection. ### Sources - - - - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Combined YAML source View the package source record on GitHub. [combined/oarfish.yml](https://github.com/mxcl/pkgdb/blob/main/combined/oarfish.yml) ## Sources - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - cross-ecosystem install command graph