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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.

If you find McCortex useful, please cite our paper:

• Integrating long-range connectivity information into de Bruijn graphs; Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics; Advanced access 15 March 2018) https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty157/4938484

Other Cortex 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