# Installer fgbio avec Homebrew Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de fgbio pour les workflows d'agents IA. ## installation ```sh sudo av install brew:fgbio ``` Commandes d'installation supplémentaires: ### macOS - Homebrew (100%): ```sh brew install fgbio ``` Preuve: local Homebrew formula metadata ## Faits du paquet - **Clé du paquet:** brew:fgbio - **Gestionnaire de paquets:** Homebrew - **Page du gestionnaire de paquets:** - **Version:** 4.1.0 - **Résumé source:** Tools for working with genomic and high throughput sequencing data - **Page d'accueil:** - **Dépôt:** - **Docs amont:** - **Licence:** MIT - **Archive source:** - **Dernière mise à jour:** 2026-05-20T05:30:27Z - **Généré:** 2026-07-08T18:08:21+00:00 ## exécutables - fgbio (cli) - fgbio (alias) ## Dépendances - openjdk ## Comportement d'installation - hook post-installation: non défini - Bouteille: disponible sur all ## Version et fraîcheur - page générée: 2026-07-08 - version du gestionnaire: 4.1.0 - gestionnaire mis à jour: 2026-05-20 - données locales: OK - dépôt amont: https://github.com/fulcrumgenomics/fgbio - info: No cached GitHub release or tag data was available. ## Historique du projet et usages fgbio is a Fulcrum Genomics toolkit for analyzing genomic and high-throughput sequencing data. It is a command-line collection aimed at read-level and variant-level workflows, with a particular emphasis on robust NGS processing, molecular indexes, and consensus-read generation. ### 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-.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 - - - - - - ## Notes de sécurité Aucun manifest local de gestion des secrets correspondant n'a été trouvé pour fgbio. Les métadonnées de paquet Nucleus restent publiées ici afin que la couverture future dispose d'une URL stable. ## Détails de la base source - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** fgbio - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Liens liés - [Source-control packages](https://www.automicvault.com/fr/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/fr/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/fr/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Database and data packages](https://www.automicvault.com/fr/pkg/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [openjdk](https://www.automicvault.com/fr/pkg/brew/openjdk/) - Runtime dependency declared by Homebrew. - [bbtools](https://www.automicvault.com/fr/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [bowtie2](https://www.automicvault.com/fr/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [cutadapt](https://www.automicvault.com/fr/pkg/brew/cutadapt/) - Shares av.db curated category or tags: bioinformatics, cli, ngs, science, sequencing. - [htslib](https://www.automicvault.com/fr/pkg/brew/htslib/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [sambamba](https://www.automicvault.com/fr/pkg/brew/sambamba/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [samtools](https://www.automicvault.com/fr/pkg/brew/samtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [sickle](https://www.automicvault.com/fr/pkg/brew/sickle/) - Shares av.db curated category or tags: bioinformatics, cli, ngs, science, sequencing. - [abricate](https://www.automicvault.com/fr/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [fastqc](https://www.automicvault.com/fr/pkg/brew/fastqc/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, data, high, openjdk. ## Combined YAML source View the package source record on GitHub. [combined/fgbio.yml](https://github.com/automic-vault/db/blob/main/combined/fgbio.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