Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.

A beta release of cortex_con is now available (new paired-end module and color-space support coming up soon).

To get to the main cortex_var page click here.

• Variant discovery by de novo assembly - no reference genome required
• Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them.
• Capable of calling SNPs, indels, inversions, complex variants, small haplotypes
• Capable of aligning a reference genome to a graph and using that to call variants
• Support for comparing cases/controls or phenotyped strains
• Integration of population information allows accurate classification of bubbles as polymorphism, error or repeat, without the use of a reference genome
• Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM