Circlator is an automated tool for circularizing genome assemblies using long sequencing reads. It was developed to address the challenge of accurately representing circular DNA structures, such as bacterial chromosomes, plasmids, and mitochondrial genomes, which are often misassembled by existing methods. The tool uses local assemblies of corrected long reads at contig ends to circularize contigs, avoiding the need to search for common sequences between low-quality ends. It was evaluated on 14 bacterial genomes, the apicoplast and mitochondria of Plasmodium falciparum, and the human mitochondrion, and outperformed existing methods like BLAST and Minimus2 in circularization accuracy. Circlator correctly circularized 22 of 23 circularizable contigs, compared to 10/24 for Minimus2 and 18/22 for BLAST. It also addressed issues such as false circularization of non-circular contigs and misassemblies in small plasmids. The tool was implemented with a workflow that includes merging contigs, local assembly, circularization, and refinement. It is available as open-source software under the GPLv3 license. Circlator improves the accuracy of genome assemblies by correcting errors in the final step of circularization, making it a valuable tool for automated genome assembly and analysis.Circlator is an automated tool for circularizing genome assemblies using long sequencing reads. It was developed to address the challenge of accurately representing circular DNA structures, such as bacterial chromosomes, plasmids, and mitochondrial genomes, which are often misassembled by existing methods. The tool uses local assemblies of corrected long reads at contig ends to circularize contigs, avoiding the need to search for common sequences between low-quality ends. It was evaluated on 14 bacterial genomes, the apicoplast and mitochondria of Plasmodium falciparum, and the human mitochondrion, and outperformed existing methods like BLAST and Minimus2 in circularization accuracy. Circlator correctly circularized 22 of 23 circularizable contigs, compared to 10/24 for Minimus2 and 18/22 for BLAST. It also addressed issues such as false circularization of non-circular contigs and misassemblies in small plasmids. The tool was implemented with a workflow that includes merging contigs, local assembly, circularization, and refinement. It is available as open-source software under the GPLv3 license. Circlator improves the accuracy of genome assemblies by correcting errors in the final step of circularization, making it a valuable tool for automated genome assembly and analysis.