Revision as of 02:02, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
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cgatools website  

The Complete Genomics Analysis Tools (cgatools) is an open source project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities, but a C++ API is available as well. The general areas of functionality include genome comparison, format conversion, and reference tools.

Available versions


Execution Environment and Modules

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

Get module information for cgatools:

$module spider cgatools

Load the default application module:

$module load cgatools

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

  • HPC_CGATOOLS_DIR - directory where cgatools is located.
  • HPC_CGATOOLS_BIN - executable directory
  • HPC_CGATOOLS_INC - includes directory
  • HPC_CGATOOLS_DOC - documentation directory


If you publish research that uses cgatools you have to cite it as follows: R. Drmanac, et. al. Science 327(5961), 78. [DOI: 10.1126/science.1181498]