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Install perbase with Homebrew

Fast and correct perbase BAM/CRAM analysis. Version 1.4.0 via Homebrew; verified 2026-09-13.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install perbase

local Homebrew formula metadata

overview

Package summary

Fast and correct perbase BAM/CRAM analysis

Commands and aliases

  • perbase

history

Project history and usage

perbase is a highly parallel Rust command-line toolkit for computing per-base metrics from BAM and CRAM files.

Project history

Seth Stadick created perbase as a highly parallel utility for per-position and per-nucleotide analysis of BAM and CRAM alignment data. The project emphasizes scalable concurrency and counting behavior intended to avoid accuracy problems identified in some existing depth tools.

Adoption history

The official project documents installation through Bioconda, Cargo, Homebrew, or downloadable release binaries, giving it several routes into genomics workflows.

How it is used

Commonly used to calculate nucleotide-resolved depth, restrict analysis to BED or VCF/BCF positions, account for overlapping mates, and emit compressed tabular output suitable for tabix indexing.

Why package nerds care

It is a Rust-based genomics CLI distributed across both language-specific and scientific package ecosystems. Its explicit treatment of deletions, reference skips, mate overlap, compression, and indexing makes it interesting to users who care about reproducible low-level sequencing metrics.

Timeline

  • 2023: perbase 0.9.0 was used by the Nano-DMS-MaP project.
  • Current project: Available through Bioconda, Cargo, Homebrew, and GitHub releases.

Related projects

  • The official README compares aspects of its counting behavior with bam-readcount and sambamba.
  • tabix is documented for indexing and querying compressed perbase output.

Sources

  • Official repository and README: https://github.com/sstadick/perbase

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Build metadata lists 3 build dependencies.

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

CommandKindExposureNote
perbasecliglobal executable

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 generated2026-09-19
manager version1.4.0
manager updated2026-09-13
local dataok
upstreamcurrent
latest detectedv1.4.0

https://github.com/sstadick/perbase

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:perbase
Version1.4.0
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/perbase
Homepagehttps://github.com/sstadick/perbase
Repositoryhttps://github.com/sstadick/perbase
LicenseMIT
Source archivehttps://github.com/sstadick/perbase/archive/refs/tags/v1.4.0.tar.gz
Last updated2026-09-13T06:48:36Z
Pulseupdated
Build dependenciescmake, pkgconf, rust
Uses from macOSbzip2, curl, llvm
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Nameperbase
Version Scheme0
Revision0
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • pkgconfBuild dependency declared by Homebrew.
  • cmakeBuild dependency declared by Homebrew.
  • rustBuild dependency declared by Homebrew.

Same workflow

  • samtoolsShares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics.
  • mosdepthShares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics.
  • bedtoolsShares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science.
  • sambambaShares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science.
  • bamtoolsShares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science.
  • blastShares pkgdb curated category or tags: bioinformatics, cli, genomics, science.

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.

Used sources

  • Geiger risk classifier
  • cross-ecosystem install command graph
  • curated package history
  • package relationship graph
  • package version freshness
  • package-page enrichment
  • pkg.so package database
  • pkgdb category and tag curation