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mccortex website  

Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and without a reference genome. Between closely related samples or highly diverged ones. From bacterial to mammalian genomes. Minimal configuration. And it's free.

Environment Modules

Run module spider mccortex to find out what environment modules are available for this application.

System Variables

  • HPC_MCCORTEX_DIR - installation directory
  • HPC_MCCORTEX_BIN - executable directory


If you publish research that uses mccortex you have to cite it as follows:

Integrating long-range connectivity information into de Bruijn graphs Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics) (Advanced access 15 March 2018)