The Cortex Project is aimed at developing parallel track applications for both de novo consensus and variant assemblies.
cortex_con is for consensus assembly, while cortex_var has been designed for variant and population assembly. The former provides for varying kmer size, whilst the latter provides for both varying kmer length with colorspace support. The developers of cortex_con state that future releases will also offer colorspace support.
This tutorial presents essential information on the available executables to choose from for your analysis, as well as additional information on the Cortex Project, including manuals.
For access to cortex_con:
for access to cortex_var
Both cortex_con and cortex_var must be compiled to support various ranges of kmer size and (in the case of cortex_var) colorspace. The table below presents available binaries of both applications on the HPCC:
Using the table above, if you wish to use a kmer length of 72 in your analysis (for example) you would select either cortex_con_95 or cortex_var_95_c1 (assuming colorspace is unimportant).
For details on the science behind the Cortex Project and/or how to use either of these applications, the following my prove helpful: