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Install oarfish with Homebrew

Long read RNA-seq quantification. Version 0.10.0 via Homebrew; verified 2026-06-21.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install oarfish

local Homebrew formula metadata

overview

Package summary

Long read RNA-seq quantification

Commands and aliases

  • oarfish

history

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.

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Build metadata lists 1 build dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
oarfishcliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08
manager version0.10.0
manager updated2026-06-21
local dataok
upstreamcurrent
latest detectedv0.10.0

https://github.com/COMBINE-lab/oarfish

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:oarfish
Version0.10.0
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/oarfish
Homepagehttps://github.com/COMBINE-lab/oarfish
Repositoryhttps://github.com/COMBINE-lab/oarfish
Upstream docshttps://github.com/COMBINE-lab/oarfish#readme
LicenseBSD-3-Clause
Source archivehttps://github.com/COMBINE-lab/oarfish/archive/refs/tags/v0.10.0.tar.gz
Last updated2026-06-21T00:20:16Z
Pulseupdated
Build dependenciesrust
Uses from macOSbzip2
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Nameoarfish
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • rustBuild dependency declared by Homebrew.

Same workflow

  • flyeShares av.db curated category or tags: bioinformatics, cli, long-read-sequencing, science.
  • kallistoShares av.db curated category or tags: bioinformatics, cli, rna-seq, science.
  • rna-starShares av.db curated category or tags: bioinformatics, cli, rna-seq, science.
  • stringtieShares av.db curated category or tags: bioinformatics, cli, rna-seq, science.
  • abpoaShares av.db curated category or tags: bioinformatics, cli, science.
  • abricateShares av.db curated category or tags: bioinformatics, cli, science.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • package relationship graph
  • package version freshness
  • package-page enrichment