Installer fgbio avec Homebrew

Liens du projet

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Commandes et alias

• fgbio

Historique du projet

The GitHub repository was created in March 2016, and the first release listed by the GitHub API is 0.1.0 later that month. The README describes fgbio as a set of tools for genomic data analysis with a focus on next-generation sequencing.

The project is written in Scala, built with sbt, and distributed as an executable jar or through package managers. Its README says the repository README is mostly for developers and builders, while the project website carries detailed user documentation, per-tool usage pages, and metrics documentation.

The toolkit's stated goals are robust, well-tested tools, an easy command line, clear documentation, and open-source development for the community and Fulcrum Genomics clients. The tool list shows the project expanding into UMI handling, consensus reads, FASTQ/BAM manipulation, QC metrics, contig-name rewriting, and synthetic mixture VCF creation.

Historique d'adoption

fgbio has a narrower package footprint than general-purpose CLIs, but it is visible in bioinformatics distribution channels. Its README advertises Bioconda, Maven Central, Javadocs, Zenodo DOI metadata, and installation through conda or a minimal conda package; the batch package facts show a Homebrew formula as well.

The project README says the tools are used by Fulcrum Genomics customers and others for ad-hoc analysis and production pipelines. That positions fgbio as a practical pipeline component rather than only a reference implementation.

Modes d'utilisation

Users run fgbio as a command-line toolkit over FASTQ, SAM/BAM, VCF/BCF, and related genomic data. Common documented areas include UMI annotation and correction, grouping reads by UMI, calling molecular or duplex consensus reads, filtering and clipping BAMs, sorting and updating read groups, collecting QC metrics, and manipulating contig names.

The README documents `java -jar target/scala-2.13/fgbio-<version>.jar` for command discovery when building locally, while normal users are directed to the hosted tools documentation and package-manager installation.

Pourquoi les passionnés de paquets s'y intéressent

fgbio matters to package maintainers because it packages a JVM/Scala genomics toolkit as a reproducible command-line dependency for sequencing pipelines. Its useful surface is a large family of subcommands, so packaging quality is about making one executable reliably available with the right Java runtime rather than exposing a single algorithm.

Chronologie

• 2016: GitHub repository created and 0.1.0 released.
• 2024: Zenodo DOI metadata was present in the project README badge.
• 2026: GitHub API showed release 4.1.0 and recent repository activity.

Related projects

• fgbio relates to bioinformatics tools and formats around FASTQ, SAM/BAM, VCF/BCF, Unique Molecular Index workflows, and Fulcrum Genomics' Rust fqtk demultiplexing work mentioned in the README.

Sources

• https://github.com/fulcrumgenomics/fgbio
• https://api.github.com/repos/fulcrumgenomics/fgbio
• https://api.github.com/repos/fulcrumgenomics/fgbio/releases
• https://fulcrumgenomics.github.io/fgbio
• https://fulcrumgenomics.github.io/fgbio/tools/latest
• https://formulae.brew.sh/formula/fgbio