Welcome to Cortex

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.

cortex_con - for consensus assembly

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

cortex_var - for variant and population assembly

For information on variant-calling, genotyping, population analysis, go to the main cortex_var page by clicking here.