Circlator

Overview

• circlator: (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

Using

Use the module name circlator to discover versions available and to load the application.

The circlator application uses the bwa, prodigal, samtools, mummer4 and spades - these are automatically loaded when circlator is loaded.

Although the documentation indicates canu can be used as an alternative to spades, there is an issue that the circlator command is unable to find the version of canu and fails when canu is in your active environment. If you need to use canu then use it in a different session.

Multicore:

Some of the circlator commands can run across multiple threads:

Please see the help for the specific command for further details e.g. run circlator all --help from the command line to find more details about the --threads option.