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cap3 website  

CAP3 is a sequence assembly program. See documentation at capdoc site. Template:App Location Intel processor optimized versions of cap3 and formcon are installed at HPC.

Opteron optimized versions of these binaries are named cap3-opteron and formcon-opteron.

In addition, pcap binaries are also provided.

Running the application using modules

To use cap3 with the environment modules system at HPC the following commands are available:

Get module information for cap3:

$module spider cap3

Load the default application module:

$module load cap3

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_CAP3_DIR - directory where cap3 is located.
  • HPC_CAP3_BIN - location of the CAP3 executables directory
  • HPC_CAP3_DOC - location of the CAP3 docs directory
  • HPC_CAP3_EXAMPLE - location of the CAP3 examples directory