使用 Homebrew, Nix, apt 安装 mosdepth

项目链接

• 主页
• 软件包管理器页面

命令和别名

• mosdepth

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• https://academic.oup.com/bioinformatics/article/34/5/867/4583630
• https://github.com/brentp/mosdepth
• https://github.com/brentp/mosdepth/wiki
• https://pmc.ncbi.nlm.nih.gov/articles/PMC6030888/
• input.source_facts.package-manager