# mosdepth mit Homebrew, Nix, apt installieren Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für mosdepth in AI-Agent-Workflows. ## Installation ```sh sudo av install brew:mosdepth ``` Weitere Installationsbefehle: ### macOS - Homebrew (100%): ```sh brew install mosdepth ``` Evidenz: local Homebrew formula metadata ### Linux - Nix (92%): ```sh nix profile install nixpkgs#mosdepth ``` Evidenz: nixpkgs package indexes: pkgs/by-name/mo/mosdepth/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt (92%): ```sh sudo apt install mosdepth ``` Evidenz: Ubuntu 24.04 LTS package indexes: mosdepth from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz ## Paketfakten - **Paketschlüssel:** brew:mosdepth - **Paketmanager:** Homebrew - **Paketmanager-Seite:** - **Version:** 0.3.14 - **Quellzusammenfassung:** Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing - **Homepage:** - **Repository:** - **Lizenz:** MIT - **Quellarchiv:** - **Zuletzt aktualisiert:** 2026-07-13T04:04:09Z - **Generiert:** 2026-08-04T22:13:35+00:00 ## Executables - mosdepth (cli) - mosdepth (Alias) ## Abhängigkeiten - htslib ## Build-Abhängigkeiten - nim ## Installationsverhalten - Post-install-Hook: nicht definiert - Bottle: verfügbar auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Version und Aktualität - Seite generiert: 2026-08-04 - Manager-Version: 0.3.14 - Manager aktualisiert: 2026-07-13 - lokale Daten: OK - Upstream-Repository: https://github.com/brentp/mosdepth - neueste erkannte Version: v0.3.14 (aktuell) ## Projektgeschichte und Nutzung mosdepth is a command-line tool for fast BAM/CRAM depth and coverage calculation across whole-genome, exome, or targeted sequencing datasets. ### Projektgeschichte mosdepth was introduced by Brent S. Pedersen and Aaron R. Quinlan in a Bioinformatics paper published online in October 2017 and appearing in the March 2018 issue. The paper presented it as a quick coverage calculator for genome and exome sequencing data. The implementation is written in Nim and uses HTSlib via hts-nim. Its algorithm tracks alignment chunk starts and ends in chromosome-sized arrays rather than using a pileup engine for every read base. ### Adoptionsgeschichte mosdepth gained adoption because sequencing coverage summaries are a routine need for variant calling QC, copy-number workflows, targeted panels, exomes, and whole genomes. The paper compared mosdepth with samtools, bedtools, and sambamba and showed faster runtime on a 30x genome benchmark. The official README documents binary releases, Bioconda, Homebrew, and Docker usage, making it straightforward to package in bioinformatics environments and reproducible workflow containers. ### Wie es verwendet wird The CLI consumes position-sorted BAM or CRAM input and can report per-base depth, region summaries from BED files, fixed windows, quantized coverage, coverage thresholds, and distributions. Users choose mosdepth when they need fast genome-wide or region-based coverage calculation and can accept the memory profile of chromosome-sized arrays. ### Warum Paket-Nerds sich dafür interessieren mosdepth is notable to package maintainers because it is a compact compiled bioinformatics binary whose value comes from speed, HTSlib integration, and predictable command-line output files rather than from daemon-style services or configuration. It is also a representative Nim-based scientific CLI in package-manager ecosystems that otherwise contain many C/C++, Python, and Perl genomics tools. ### Zeitleiste - 2017: Bioinformatics article published online introducing mosdepth. - 2018: Article appears in Bioinformatics volume 34 issue 5. - 2025: GitHub wiki FAQ updated. - 2026: GitHub releases list a latest release dated April 24, 2026. ### Related projects - samtools depth, BEDTools genomecov, and sambamba are related depth/coverage tools compared in the official paper and README. - HTSlib and hts-nim are implementation dependencies named in the README and paper. ### Quellen - - - - - input.source_facts.package-manager ## Sicherheitshinweise Für mosdepth wurde kein passendes lokales Secret-Handling-Manifest gefunden. Paketmetadaten bleiben hier veröffentlicht, damit künftige Abdeckung eine stabile Paket-URL hat. ## Details aus der Quelldatenbank - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** mosdepth - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Andere Paketmanager-Einträge - Nix - mosdepth: normalized package name match | nixpkgs package indexes: pkgs/by-name/mo/mosdepth/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - mosdepth - 0.3.6+ds-1: normalized package name match | Ubuntu 24.04 LTS package indexes: mosdepth from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | BAM/CRAM depth calculation biological sequencing | https://github.com/brentp/mosdepth - Ubuntu apt - mosdepth-examples - 0.3.6+ds-1: normalized package name match | Ubuntu 24.04 LTS package indexes: mosdepth-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Test data for mosdepth | https://github.com/brentp/mosdepth ## Verwandte Links - [Source-control packages](https://pkg.so/de/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://pkg.so/de/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/de/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://pkg.so/de/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://pkg.so/de/brew/htslib/) - Runtime dependency declared by Homebrew. - [nim](https://pkg.so/de/brew/nim/) - Build dependency declared by Homebrew. - [bismark](https://pkg.so/de/brew/bismark/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, wgs. - [samtools](https://pkg.so/de/brew/samtools/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics. - [sambamba](https://pkg.so/de/brew/sambamba/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science. - [augustus](https://pkg.so/de/brew/augustus/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [perbase](https://pkg.so/de/brew/perbase/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics. - [tabixpp](https://pkg.so/de/brew/tabixpp/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [chopper](https://pkg.so/de/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://pkg.so/de/brew/minigraph/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. ## Combined YAML source View the package source record on GitHub. [combined/mosdepth.yml](https://github.com/mxcl/pkgdb/blob/main/combined/mosdepth.yml) ## Quellen - pkg.so package database - package-page enrichment - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph