Dnaapler is a flexible tool for reorienting circular microbial genomes, including bacterial chromosomes, plasmids, and bacteriophages. It addresses the issue of arbitrary start points in circular genome assemblies, which can affect downstream analysis. The tool uses BLAST or Pyrodigal to identify specific genes (dnaA, repA, terL) and reorients the genome to start at these genes. Dnaapler offers various subcommands for different reorientation strategies, including custom databases, mystery, nearest, and largest CDS. It is available on GitHub and PyPI, with continuous integration and deployment. Dnaapler has been integrated into the StaPH-B consortium Docker image collection. The tool is designed to be lightweight and easy to integrate into assembly workflows, making it a valuable resource for microbial genome analysis. Examples of its functionality are shown on the Staphylococcus aureus chromosome and the Sa3int prophage. Dnaapler provides a standardized and efficient method for reorienting circular microbial genomes, improving the accuracy and consistency of downstream analyses.Dnaapler is a flexible tool for reorienting circular microbial genomes, including bacterial chromosomes, plasmids, and bacteriophages. It addresses the issue of arbitrary start points in circular genome assemblies, which can affect downstream analysis. The tool uses BLAST or Pyrodigal to identify specific genes (dnaA, repA, terL) and reorients the genome to start at these genes. Dnaapler offers various subcommands for different reorientation strategies, including custom databases, mystery, nearest, and largest CDS. It is available on GitHub and PyPI, with continuous integration and deployment. Dnaapler has been integrated into the StaPH-B consortium Docker image collection. The tool is designed to be lightweight and easy to integrate into assembly workflows, making it a valuable resource for microbial genome analysis. Examples of its functionality are shown on the Staphylococcus aureus chromosome and the Sa3int prophage. Dnaapler provides a standardized and efficient method for reorienting circular microbial genomes, improving the accuracy and consistency of downstream analyses.