Detecting variation in genomes from bacteria to man can now be accomplished during genome assembly using an application named Cortex, according to Iqbal et al. Cortex can assemble, de novo, sequence data from multiple genomes simultaneously without the need for a reference genome. The method uses de Bruijn graphs, which provide a visual picture of regions of variation in compared sequences. Any sequence read length can be combined from short reads to fully assembled genomes. One key feature of this new approach reported by Iqbal et al. is that although regions that are variable are clearly delimited, information specific to each individual in an analyzed population can also still be accessed by associating a color with that individual. To demonstrate the versatility of Cortex, Iqbal et al. present four case study applications of Cortex, including the detection of simple and complex variations in a high-coverage genome and variation among ten chimpanzee genomes. Cortex is currently the only assembler that can assemble multiple eukaryotic genomes. It doesn't use vast computational resources and can assemble 1,000 Saccharomyces cerevisiae samples in less than 64 GB of random-access memory (RAM). Cortex could be used to detect changes between highly related genomes, for example, cancer genomes during carcinogenesis. (Nat. Genet. advance online publication, doi:10.1038/ng.1028, 8 January 2012)