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Overview

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.

Loading Cortex

For access to cortex_con:

 

module load cortex

 

for access to cortex_var

 

module load cortexVar

 

Executables Available

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:

Executable
kmer range
colorspace
cortex_con_311-31--
cortex_var_31_c11-311
cortex_con_6333-63--
cortex_var_63_c133-631
cortex_var_63_c17233-63172
cortex_con_9565-95--
cortex_var_95_c165-951
cortex_con_12797-127--
cortex_var_127_c197-1271
cortex_con_160 (1)129-159--
cortex_var_159_c1129-1591
cortex_con_192 (1)161-191--
cortex_var_191_c1161-1911
cortex_con_223193-223--
cortex_var_223_c1193-2231
cortex_con_255225-255--
cortex_var_255_c1225-2551
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(1) These 2 binaries are somewhat misnamed due to an issue with the developer's Makefile. Please refer to the kmer range in the table during the selection process.

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).

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For those interested in expanded colorspace support, please contact the HPCC to have the version you need built, or visit the developer's website to download and compile your own copy.

More Information

For details on the science behind the Cortex Project and/or how to use either of these applications, the following my prove helpful: