Autocycler: long-read consensus assembly for bacterial genomes.

ABSTRACT:

Motivation

Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using Trycycler can improve accuracy, but its lack of automation limits scalability. There is a need for an automated method to generate high-quality consensus bacterial genome assemblies from long-read data.

Results

We present Autocycler, a command-line tool for generating accurate bacterial genome assemblies by combining multiple alternative long-read assemblies of the same genome. Without requiring user input, Autocycler builds a compacted De Bruijn graph from the input assemblies, clusters and filters contigs, trims overlaps, and resolves consensus sequences by selecting the most c

SUBMITTER: Wick RR 

PROVIDER: S-EPMC12460055 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature