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Welcome to the McCortex wiki!

McCortex is a genome assembler and variant caller. It has a rich set of features for representing and manipulating genomes as graphs, correcting reads, generating haploid assemblies and calling variants. It can run with and without a reference genome. It is a re-write of the original Cortex Assembler.

Check out Installation, Workflow Examples and running the McCortex Pipeline. More information in the Glossary, on file formats and the McCortex webserver.

If you find a bug, please submit it as an Issue on github.

For a list of authors please see the Authors file.

McCortex is released under the MIT license. To find out more about the code please read the Contributing page.