macOS
Homebrewverified · 100%
brew install picard-toolslocal Homebrew formula metadata
brew / rank 6622
Install picard-tools with Homebrew, apt, Nix, apk, chocolatey, dnf, pacman, zypper, scoop, winget
Tools for manipulating HTS data and formats. Version 3.5.0 via Homebrew; verified 2026-07-31. Also installable with debian: sudo apt install libpicard-java.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install picard-toolsDebian stable package indexes · picard-tools · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#picard-toolsnixpkgs package indexes · pkgs/by-name/pi/picard-tools/package.nix · source: api.github.com
Alpine Linux apkverified · 92%
sudo apk add picardAlpine Linux edge package indexes · picard · source: dl-cdn.alpinelinux.org
Fedora dnfverified · 92%
sudo dnf install picardFedora Rawhide package metadata · picard · source: dl.fedoraproject.org
Arch Linux pacmanverified · 92%
sudo pacman -S picardArch Linux sync databases · picard · source: geo.mirror.pkgbuild.com
openSUSE zypperverified · 92%
sudo zypper install picardopenSUSE Tumbleweed package metadata · picard · source: download.opensuse.org
Windows
Chocolateyverified · 92%
choco install picardChocolatey community package catalog · picard · source: community.chocolatey.org
Scoopverified · 92%
scoop install extras/picardScoop official bucket manifest trees · bucket/picard.json · source: api.github.com
Windows Package Managerverified · 92%
winget install --id MusicBrainz.Picard -eWindows Package Manager source index · MusicBrainz.Picard · source: cdn.winget.microsoft.com
overview
Package summary
Tools for manipulating HTS data and formats
Project links
Commands and aliases
- picard
history
Project history and usage
Picard Tools is the Broad Institute's Java command-line toolkit for manipulating, validating, converting, and collecting metrics from high-throughput sequencing data.
Project history
Picard Tools is the Broad Institute's Java toolkit for manipulating high-throughput sequencing formats including SAM, BAM, CRAM, and VCF. The current public repository was established in 2014, while the toolkit belongs to the older Broad sequencing-analysis ecosystem.
Picard is implemented on HTSJDK, the Java library for accessing common sequencing formats. Its tools later became closely integrated with GATK; GATK 4 describes its mission as bringing together established GATK and Picard tools under a streamlined framework.
Adoption history
Picard became a standard component of next-generation sequencing preprocessing because it groups many format-aware operations into one toolkit: read-group editing, sorting, conversion, duplicate marking, validation, interval handling, and sequencing QC metrics.
The Broad Institute's GATK 4 project explicitly brings together established tools from the GATK and Picard codebases. Picard is also broadly distributed through scientific and general-purpose package ecosystems, making its command semantics common in reproducible genomics pipelines.
How it is used
Practitioners invoke individual tools through the Picard jar or a package-manager-provided picard wrapper. Common pipeline steps include adding read groups, sorting alignments, marking duplicates, validating SAM/BAM files, converting formats, manipulating interval lists, and producing library or sequencing metrics.
Picard is most often scripted between alignment and variant analysis. It has no general per-user configuration or credential file; behavior is supplied through command options, JVM arguments, input data, references, and environment-specific cloud authentication when applicable.
Why package nerds care
Picard is package-nerd significant because it combines a large family of narrowly scoped scientific commands in one Java artifact. Pipeline maintainers care about its Java runtime, HTSJDK compatibility, strict format validation, reference and index assumptions, metrics outputs, and behavior changes that can affect reproducibility.
Its best-known command, MarkDuplicates, made Picard a standard reference point for duplicate-marking implementations. The package often sits between an aligner and downstream variant calling, where metadata and file-format correctness are part of the scientific record.
Timeline
- 2014: The current broadinstitute/picard public repository was established.
- 2019: The official repository documented Picard Toolkit as its recommended software citation.
- GATK 4 era: Established Picard tools were incorporated into the unified GATK framework.
- 2020s: Picard continued evolving with HTSJDK, Java, BAM, CRAM, and cloud-I/O changes.
Related projects
- HTSJDK supplies Picard's Java format-access layer.
- GATK incorporates established Picard tools into a broader variant-discovery toolkit.
- The hts-specs project defines the SAM, BAM, CRAM, and VCF formats that Picard processes.
Sources
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 1 platform targets.
- Installs with 1 runtime 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
| Command | Kind | Exposure | Note |
|---|---|---|---|
picard | cli | global 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 generated2026-11-04
manager version3.5.0
manager updated2026-07-31
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/broadinstitute/picard
- infoNo cached GitHub release or tag data was available.https://github.com/broadinstitute/picardnone confidence
install metadata
Package metadata
| Package key | brew:picard-tools |
|---|---|
| Version | 3.5.0 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/picard-tools |
| Homepage | https://broadinstitute.github.io/picard/ |
| Repository | https://github.com/broadinstitute/picard |
| Upstream docs | https://broadinstitute.github.io/picard/ |
| License | MIT |
| Source archive | https://github.com/broadinstitute/picard/releases/download/3.5.0/picard.jar |
| Last updated | 2026-07-31T21:30:01Z |
| Pulse | updated |
| Dependencies | openjdk |
| Bottle | available (on all) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | picard-tools |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
libpicard-java 3.3.0+dfsg-2
Java library to manipulate SAM and BAM files
https://broadinstitute.github.io/picard/
sudo apt install libpicard-java- Section: java
- Architecture: all
- Source Package: picard-tools
- 6 dependencies
- 2 optional deps
- normalized package name match
- Matched by: Picard Tools
Debian apt95%
libpicard-java-doc 3.3.0+dfsg-2
Documentation for the java picard library
https://broadinstitute.github.io/picard/
sudo apt install libpicard-java-doc- Section: doc
- Architecture: all
- Source Package: picard-tools
- 1 dependencies
- normalized package name match
- Matched by: Picard Tools
Debian apt95%
picard-tools 3.3.0+dfsg-2
Command line tools to manipulate SAM and BAM files
https://broadinstitute.github.io/picard/
sudo apt install picard-tools- Section: science
- Architecture: all
- 3 dependencies
- normalized package name match
- Matched by: Picard Tools
Nix95%
picard-tools
nix profile install nixpkgs#picard-tools- normalized package name match
- Matched by: Picard Tools
Ubuntu apt95%
libpicard-java 3.1.1+dfsg-1
Java library to manipulate SAM and BAM files
https://broadinstitute.github.io/picard/
sudo apt install libpicard-java- Section: universe/java
- Architecture: all
- Source Package: picard-tools
- 6 dependencies
- 2 optional deps
- normalized package name match
- Matched by: Picard Tools
Ubuntu apt95%
libpicard-java-doc 3.1.1+dfsg-1
Documentation for the java picard library
https://broadinstitute.github.io/picard/
sudo apt install libpicard-java-doc- Section: universe/doc
- Architecture: all
- Source Package: picard-tools
- 1 dependencies
- normalized package name match
- Matched by: Picard Tools
Ubuntu apt95%
picard-tools 3.1.1+dfsg-1
Command line tools to manipulate SAM and BAM files
https://broadinstitute.github.io/picard/
sudo apt install picard-tools- Section: universe/science
- Architecture: all
- 3 dependencies
- normalized package name match
- Matched by: Picard Tools
Debian apt92%
picard 2.13.3-1
Next-Generation MusicBrainz audio files tagger
https://picard.musicbrainz.org/
sudo apt install picard- Section: sound
- Architecture: amd64
- 12 dependencies
- 3 optional deps
- installed executable or alias match
- Matched by: Picard
Nix92%
picard
nix profile install nixpkgs#picard- installed executable or alias match
- Matched by: Picard
Ubuntu apt92%
picard 2.11-1
Next-Generation MusicBrainz audio files tagger
https://picard.musicbrainz.org/
sudo apt install picard- Section: universe/sound
- Architecture: amd64
- 13 dependencies
- 3 optional deps
- installed executable or alias match
- Matched by: Picard
apk92%
picard 2.13.3_git20251006-r2
Official MusicBrainz tagger
https://picard.musicbrainz.org/
sudo apk add picard- License: GPL-2.0-or-later
- Architecture: x86_64
- Source Package: picard
- 1 dependencies
- 1 provides
- installed executable or alias match
- Matched by: Picard
apk92%
picard-lang 2.13.3_git20251006-r2
Official MusicBrainz tagger
https://picard.musicbrainz.org/
sudo apk add picard-lang- License: GPL-2.0-or-later
- Architecture: x86_64
- Source Package: picard
- 1 dependencies
- installed executable or alias match
- Matched by: Picard
apk92%
picard-pyc 2.13.3_git20251006-r2
Precompiled Python bytecode for picard
https://picard.musicbrainz.org/
sudo apk add picard-pyc- License: GPL-2.0-or-later
- Architecture: x86_64
- Source Package: picard
- 1 dependencies
- installed executable or alias match
- Matched by: Picard
dnf92%
picard 2.13.3-9.fc45
MusicBrainz-based audio tagger
https://github.com/musicbrainz/picard
sudo dnf install picard- License: GPL-2.0-or-later
- Category: Unspecified
- Architecture: x86_64
- Source Package: picard
- 11 dependencies
- 6 provides
- installed executable or alias match
- Matched by: Picard
pacman92%
picard 2.13.3-3
Official MusicBrainz tagger
https://github.com/metabrainz/picard
sudo pacman -S picard- License: GPL-2.0-or-later
- Architecture: x86_64
- 11 dependencies
- 3 optional deps
- installed executable or alias match
- Matched by: Picard
zypper92%
picard 2.13.3-1.7
The Next Generation MusicBrainz Tagger
https://picard.musicbrainz.org
sudo zypper install picard- License: GPL-2.0-or-later
- Category: Productivity/Multimedia/Sound/Utilities
- Architecture: x86_64
- Source Package: picard
- 12 dependencies
- 6 provides
- installed executable or alias match
- Matched by: Picard
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
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment
- pkg.so package database
- pkgdb category and tag curation