Autocycler (Flye)Fast Autocycler with Flye fallback pipeline on long reads from one bacterial isolate. Builds Flye and multi-assembler Autocycler assemblies, selects a fully resolved Autocycler consensus within the genome-size bounds when available, and otherwise selects Flye. Also reports per-contig depth, copy number and PLSDB similarity.Versions

v0.8.0 (default)

Tags: ONT, PacBio, Bacteria, Assembly, Consensus assembly, Genome size estimation, Plasmid similarity screening, cpgParameters

reads (file) required: Quality-controlled long reads from one bacterial isolate. BAM input must be unaligned BAM (uBAM).

read_type (enum) required: Long-read technology and chemistry. Options: ont_r9, ont_r10, pacbio_clr, pacbio_hifi

genome_size (int): Optional genome size in base pairs. Leave empty to estimate using Raven.

Links

License: GPL-3.0-or-later

Cite as: Wick RR, Howden BP, Stinear TP. (2025). Autocycler: long-read consensus assembly for bacterial genomes. *Bioinformatics* 41(9), btaf474. https://doi.org/10.1093/bioinformatics/btaf474 Also cite Flye, Plassembler and the other assemblers used by the pipeline.

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