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brew install autocyclerlocal Homebrew formula metadata
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Install autocycler with Homebrew
Tool for generating consensus long-read assemblies for bacterial genomes. Version 0.6.2 via Homebrew; verified 2026-04-14.
install
Additional install commands
overview
Package summary
Tool for generating consensus long-read assemblies for bacterial genomes
Project links
Commands and aliases
- autocycler
history
Project history and usage
Autocycler is a Rust command-line tool for generating consensus long-read bacterial genome assemblies from multiple alternative assemblies.
Project history
The GitHub repository was created on 2023-11-10 and the first public GitHub release, v0.1.0, was published on 2024-11-11. The README describes Autocycler as the successor to Trycycler and says most users should prefer Autocycler over Trycycler.
In 2025, Wick, Howden and Stinear published the Autocycler paper in Bioinformatics, giving the project a formal citation path for research use. By 2026 the project had reached v0.6.2, published on 2026-04-14.
Adoption history
Autocycler's adoption path is academic and bioinformatics-oriented: the README asks research users to cite the Bioinformatics paper, the wiki provides workflows for automated and manually curated assemblies, and the installation docs mention Bioconda in addition to pre-built binaries.
Its scope is intentionally narrower than general genome assembly: the wiki says it aims to produce complete bacterial genome assemblies and requires input assemblies that are mostly or ideally all complete.
How it is used
The wiki describes a multi-step workflow: subsample reads, generate several input assemblies with supported long-read assemblers, compress assemblies into a unitig graph, cluster contigs, trim and resolve clusters, then combine resolved clusters into consensus_assembly.fasta.
For minimal setup, the very quick start points users at a conda environment and an automated Bash pipeline that runs the full process with reads.fastq.gz, thread count and parallel job count.
Why package nerds care
Autocycler is notable for packaging a modern Rust bioinformatics executable whose usefulness depends on a surrounding toolchain of long-read assemblers. The binary itself is standalone, but real-world workflows often rely on conda environments, Dockerfiles or pipeline scripts to assemble the full stack.
For package databases, it is a good example of a domain-specific CLI where the Homebrew formula exposes only one executable while the official docs point to Bioconda and custom environments for complete scientific workflows.
Timeline
- 2023: GitHub repository created on 2023-11-10.
- 2024: v0.1.0 released on 2024-11-11.
- 2025: Autocycler paper published in Bioinformatics.
- 2026: v0.6.2 released on 2026-04-14.
Related projects
- The README identifies Trycycler as Autocycler's predecessor.
- The wiki's automated workflow references long-read assemblers including canu, flye, metamdbg, miniasm, necat, nextdenovo, plassembler and raven.
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 6 platform targets.
- Build metadata lists 1 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
| Command | Kind | Exposure | Note |
|---|---|---|---|
autocycler | 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 generated2026-07-08
manager version0.6.2
manager updated2026-04-14
local dataok
upstreamcurrent
latest detectedv0.6.2
https://github.com/rrwick/Autocycler
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:autocycler |
|---|---|
| Version | 0.6.2 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/autocycler |
| Homepage | https://github.com/rrwick/Autocycler |
| Repository | https://github.com/rrwick/Autocycler |
| Upstream docs | https://github.com/rrwick/Autocycler/wiki |
| License | GPL-3.0-or-later |
| Source archive | https://github.com/rrwick/Autocycler/archive/refs/tags/v0.6.2.tar.gz |
| Last updated | 2026-04-14T10:27:47Z |
| Pulse | updated |
| Build dependencies | rust |
| 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 | autocycler |
| Version Scheme | 0 |
| Revision | 0 |
| Head Version | HEAD |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
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
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- package relationship graph
- package version freshness
- package-page enrichment