# Install mosdepth with Homebrew, Nix, apt Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. Version 0.3.14 via Homebrew; verified 2026-07-13. Also installable with nix: nix profile install nixpkgs#mosdepth. ## Install ```sh sudo av install brew:mosdepth ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install mosdepth ``` Evidence: local Homebrew formula metadata ### Linux - Nix (92%): ```sh nix profile install nixpkgs#mosdepth ``` Evidence: 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 ``` Evidence: Ubuntu 24.04 LTS package indexes: mosdepth from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz ## Package facts - **Package key:** brew:mosdepth - **Package manager:** Homebrew - **Version:** 0.3.14 - **Source summary:** Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing - **Homepage:** - **Repository:** - **Last updated:** 2026-07-13T04:04:09Z - **Generated:** 2026-08-03T19:37:03+00:00 ## Executables - mosdepth (alias) ## Install behavior - Bottle: not available ## Freshness - Page generated: 2026-08-03 - Package-manager version: 0.3.14 ## Project history and usage mosdepth is a command-line tool for fast BAM/CRAM depth and coverage calculation across whole-genome, exome, or targeted sequencing datasets. ### Project history 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. ### Adoption history 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. ### How it is used 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. ### Why package nerds care 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. ### Timeline - 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. ### Sources - - - - - input.source_facts.package-manager ## Security Notes No matching local secret-handling manifest was found for mosdepth. Nucleus package metadata is still published here so future coverage has a stable package URL. ## Other Package-Manager Records - 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 ## Combined YAML source View the package source record on GitHub. [combined/mosdepth.yml](https://github.com/mxcl/pkgdb/blob/main/combined/mosdepth.yml) ## Sources - pkg.so package database - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph