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Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.
NOVOPlasty - The organelle assembler and heteroplasmy caller. NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes..