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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 including:

• correcting reads
• genome assembly
• calling variants
• genotyping 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.

Got a question? Check out the FAQs. 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.

'Cortex with low memory and read threading' is currently unpublished. Please cite previous cortex_var papers:

• De novo assembly and genotyping of variants using colored de Bruijn graphs, Iqbal(), Caccamo(), Turner, Flicek, McVean (Nature Genetics) (2012) (doi:10.1038/ng.1028) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272472
• High-throughput microbial population genomics using the Cortex variation assembler, Iqbal, Turner, McVean (Bioinformatics) (Nov 2012) (doi:10.1093/bioinformatics/bts673) http://www.ncbi.nlm.nih.gov/pubmed/23172865