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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 and on file formats.

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.