macOS
Homebrewverified · 100%
brew install sicklelocal Homebrew formula metadata
brew / rank 13587
Install sickle with Homebrew, apt
Windowed adaptive trimming for FASTQ files using quality. Version 1.33 via Homebrew; verified 2026-09-13. Also installable with debian: sudo apt install sickle.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install sickleDebian stable package indexes · sickle · source: deb.debian.org
overview
Package summary
Windowed adaptive trimming for FASTQ files using quality
Project links
Commands and aliases
- sickle
history
Project history and usage
Sickle is a C command-line program that trims low-quality sequence from FASTQ reads with an adaptive sliding-window algorithm and discards reads below a chosen length threshold.
Project history
Najoshi and Fass developed Sickle as a sliding-window, adaptive quality trimmer for FASTQ sequencing reads. Upstream's requested software citation dates the project to 2011 and identifies version 1.33.
Adoption history
Sickle became available through bioinformatics and operating-system packaging channels. The supplied metadata records Homebrew, Debian, and Ubuntu packages, while the official repository includes an XML descriptor for integration into local Galaxy installations.
How it is used
Sickle offers `se` and `pe` modes for single-end and paired-end reads. Users specify FASTQ inputs, quality encoding, output files, and optional quality or length thresholds; paired-end mode can preserve pairs, emit orphaned reads separately, or produce interleaved output.
Why package nerds care
Sickle captures an earlier generation of compact, native bioinformatics command-line tools: a focused C executable, compressed-FASTQ support through zlib, explicit quality-encoding selection, and straightforward composition in sequencing pipelines. Its Galaxy descriptor also bridges shell-oriented and workflow-platform packaging.
Timeline
- 2011: Upstream's requested citation dates Sickle and version 1.33 to this year.
- Subsequent packaging: Sickle became available through Homebrew, Debian, and Ubuntu.
Related projects
- Galaxy can expose Sickle through the XML tool descriptor shipped in the repository.
- kseq.h, bundled with the source, provides sequence parsing.
- zlib provides compressed-input support.
Sources
- https://github.com/najoshi/sickle#readme
- source_facts.package-manager
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.
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 |
|---|---|---|---|
sickle | 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 generated2026-09-19
manager version1.33
manager updated2026-09-13
local dataok
upstreamcurrent
latest detectedv1.33
https://github.com/najoshi/sickle
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:sickle |
|---|---|
| Version | 1.33 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/sickle |
| Homepage | https://github.com/najoshi/sickle |
| Repository | https://github.com/najoshi/sickle |
| License | MIT |
| Source archive | https://github.com/najoshi/sickle/archive/refs/tags/v1.33.tar.gz |
| Last updated | 2026-09-13T09:05:23Z |
| Pulse | updated |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | sickle |
| 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%
sickle 1.33+git20150314.f3d6ae3-2
windowed adaptive trimming tool for FASTQ files using quality
https://github.com/najoshi/sickle
sudo apt install sickle- Section: science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Sickle
Ubuntu apt95%
sickle 1.33+git20150314.f3d6ae3-2
windowed adaptive trimming tool for FASTQ files using quality
https://github.com/najoshi/sickle
sudo apt install sickle- Section: universe/science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Sickle
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