使用 Homebrew 安装 autocycler

项目链接

• 主页
• 上游文档
• 软件包管理器页面

命令和别名

• autocycler

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• https://api.github.com/repos/rrwick/Autocycler
• https://api.github.com/repos/rrwick/Autocycler/releases
• https://doi.org/10.1093/bioinformatics/btaf474
• https://github.com/rrwick/Autocycler#readme
• https://github.com/rrwick/Autocycler/wiki