rrwick/Autocycler

A tool for generating consensus long-read assemblies for bacterial genomes

239

stars

453

commits

Rust

primary language

Aug 31, 2026

updated

README

Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes. It is the successor to Trycycler, and for most users, I recommend Autocycler over Trycycler.

For installation instructions, usage, deeper explanations and more, head over to the Autocycler wiki!

If you use Autocycler in your research, please cite the following paper:
Wick RR, Howden BP, Stinear TP (2025). Autocycler: long-read consensus assembly for bacterial genomes. Bioinformatics. doi:10.1093/bioinformatics/btaf474.

Contributors

442 commits

4 commits

2 commits

1 commits

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Shell

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rrwick/Autocycler

A tool for generating consensus long-read assemblies for bacterial genomes

239

stars

453

commits

Rust

primary language

Aug 31, 2026

updated

README

Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes. It is the successor to Trycycler, and for most users, I recommend Autocycler over Trycycler.

For installation instructions, usage, deeper explanations and more, head over to the Autocycler wiki!

Similar repos

rrwick/Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

349

same org

BirolLab/arcs

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

BirolLab/abyss

:microscope: Assemble large genomes using short reads

333

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

186

ncbi/amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes…

392

BirolLab/tigmint

⛓ Correct misassemblies using linked AND long reads

ncbi/fcs

Foreign Contamination Screening caller scripts and documentation

175

tseemann/abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

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Contributors

442 commits

4 commits

2 commits

1 commits

Languages

Rust

88.4%

Python

5.9%

Shell

4.9%