Install oarfish with Homebrew

Project links

• Homepage

Commands and aliases

• oarfish

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

• https://academic.oup.com/bioinformatics/article/41/Supplement_1/i304/8199410
• https://api.github.com/repos/COMBINE-lab/oarfish
• https://bioconda.github.io/recipes/oarfish/README.html
• https://formulae.brew.sh/formula/oarfish
• https://github.com/COMBINE-lab/oarfish
• https://github.com/COMBINE-lab/oarfish/releases
• https://pubmed.ncbi.nlm.nih.gov/38464200/
• https://www.biorxiv.org/content/10.1101/2024.02.28.582591v1