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Corticall: A graph-based de novo mutation caller based on traversing (Mc)Cortex de novo assembly graph and link data.

Quick start

git clone
cd Corticall
java -jar dist/corticall.jar -h


Corticall is a Java-based de novo mutation (DNM) caller based on linked multi-color de Bruijn graphs (LdBG) produced by McCortex. It is able to leverage multiple reference sequences to better characterize DNMs in otherwise inaccessible regions of canonical reference genomes.

Corticall may also be used as a class library for performing efficient, low-memory traversals on LdBGs. The most important functionalities provided are:

  • iterating over records in a Cortex graphs
  • random access (by binary search) to Cortex graph records
  • performing simple walks (i.e. extracting a contig, optionally using links to disambiguate junction choices)
  • performing walks assisted by one or more reference sequences in a manner consistent with link information
  • performing depth-first searches with custom stopping rules (useful for finding interesting graph motifs)
  • aligning k-mers and contigs back to reference sequences

Corticall handles the heavy lifting when operating with these data structures, permitting developers to concentrate on the genome analysis and variant calling tools that can be written on top of this API.


Corticall is released under the Apache 2.0 license. The latest code is freely available at Github.


Corticall has the following dependencies:

  • Java8: needed for runtime and development kit
  • Apache Ant: for dependency fetching and compilation

Additional recommended software:

  • McCortex: for building Cortex graphs and link annotations


To download and compile:

git clone
cd Corticall

To run (and get a listing of available commands):

java -jar dist/corticall.jar

To get help for a specific command (e.g. "Call"):

java -jar dist/corticall.jar Call


Please contact Kiran V Garimella ( with any questions/comments/concerns/cake. Feedback, bug reports, and pull requests are welcome.

Related projects

For a pythonic take on programmatically accessing McCortex linked multi-color de Bruijn graphs, see Winni Kretzschmar's cortexpy project.


The original multi-color de Bruijn graph paper can be found at:

Our manuscript on linked multi-color de Bruijn graphs is now available via Bioinformatics at:

A manuscript preprint for Corticall, our de novo assembly approach to de novo mutation detection in pathogens, can be found at:

  • "Detection of simple and complex de novo mutations without, with, or with multiple reference sequences", Garimella, Iqbal, Krause, Campino, Kekre, Drury, Kwiatkowski, Sa, Wellems, McVean (2019) (doi:10.1101/698910)