macOS
Homebrewverified · 100%
brew install mosdepthlocal Homebrew formula metadata
brew / rank 13013
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
Additional install commands
Linux
Nixverified · 92%
nix profile install nixpkgs#mosdepthnixpkgs package indexes · pkgs/by-name/mo/mosdepth/package.nix · source: api.github.com
Ubuntu aptverified · 92%
sudo apt install mosdepthUbuntu 24.04 LTS package indexes · mosdepth · source: archive.ubuntu.com
overview
Package summary
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Project links
Commands and aliases
- mosdepth
history
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
security posture
No protected-tool coverage found yet
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.
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
mosdepth | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version0.3.14
manager updated2026-07-13
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:mosdepth |
|---|---|
| Version | 0.3.14 |
| Package manager | Homebrew |
| Homepage | https://github.com/brentp/mosdepth |
| Repository | https://github.com/brentp/mosdepth |
| Last updated | 2026-07-13T04:04:09Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Nix95%
mosdepth
nix profile install nixpkgs#mosdepth- normalized package name match
- Matched by: Mosdepth
Ubuntu apt95%
mosdepth 0.3.6+ds-1
BAM/CRAM depth calculation biological sequencing
https://github.com/brentp/mosdepth
sudo apt install mosdepth- Section: universe/science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Mosdepth
Ubuntu apt95%
mosdepth-examples 0.3.6+ds-1
Test data for mosdepth
https://github.com/brentp/mosdepth
sudo apt install mosdepth-examples- Section: universe/science
- Architecture: all
- Source Package: mosdepth
- normalized package name match
- Matched by: Mosdepth
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation