First install Docker, then install circlator: docker pull sangerpathogens/circlator If the tests all pass, install: python3 setup.py installĬirclator can be run in a Docker container. Then run the tests: python3 setup.py test Once the dependencies are installed, install Circlator using pip3: pip3 install circlator Otherwise, Circlator will look for spades.py in your $PATH. If this environment variable is set, then it is used by Circlator. Note that you can use the environment variable $CIRCLATOR_SPADES to specify the name of the SPAdes exectuable. Publication, tested on all SPAdes versions 3.6.2-3.9.0). ![]() SPAdes version 3.6.2 or higher is required, butģ.7.1 is recommended (marginally gave the best results on NCTC data from the Circlator Installation Using pip or from sourceĬirclator has the following dependencies, which need to be installed first (you will need SPAdes or Canu: ![]() doi: 10.1186/s1305-0.įor how to use Circlator, please see the Circlator wiki page. The algorithm and benchmarks are described in theĬitation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al,
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