Alternative name: McCortex | cortex_var
Allows de novo genome assembly and multisample variant calling. Cortex is a modular set of multi-threaded programs for manipulating assembly graphs. Linked de Bruijn Graph (LdBG) data structure and associated algorithms are implemented as part of the software. It was used for two tasks where long-range information is likely to be beneficial: finding large differences from a reference and analysis of genomic context for drug resistance genes, which was validated using a PacBio reference assembled for the sample.