DOCUMENTATION

http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/

This code is no longer in active development. Pull requests and bugs will be addressed as needed.

Plotting

The authors recommend using IGV to view the output.

http://www.broadinstitute.org/igv/

Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.

LICENSE

/*

• Copyright (C) 2010,2011,2012 Scott Clark. All rights reserved.
• Developed by:
• Scott Clark
• Cornell University Center for Applied Mathematics
• http://cam.cornell.edu
• AND
• Rob Egan
• Department of Energy Joint Genome Institute
• http://jgi.doe.gov
• Permission is hereby granted, free of charge, to any person obtaining a
• copy of this software and associated documentation files (the "Software"),
• to deal with the Software without restriction, including without limitation
• the rights to use, copy, modify, merge, publish, distribute, sublicense,
• and/or sell copies of the Software, and to permit persons to whom the
• Software is furnished to do so, subject to the following conditions:
• 1. Redistributions of source code must retain the above copyright notice,

•  this list of conditions and the following disclaimers.
  

• 2. Redistributions in binary form must reproduce the above copyright

•  notice, this list of conditions and the following disclaimers in the 
  

•  documentation and/or other materials provided with the distribution.
  

• 3. Neither the names of Cornell University, The Joint Genome Institute,

•  nor the names of its contributors may be used to endorse or promote 
  

•  products derived from this Software without specific prior written 
  

•  permission.
  

• THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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// For more information on the licence please see // The University of Illinois/NCSA Open Source License // http://www.opensource.org/licenses/UoI-NCSA.php

INSTALL

http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#installation

ALE comes packaged with samtools-0.1.18 Feel free to use a later version

samtools is open source (MIT license)

We would like to thank the creators for the extensive and very useful package

Requirements for plotter4.py: numpy 1.6.1 mpmath 0.17 setuptools 0.6c11 matplotlib 1.0.1 pymix 0.8 http://www.pymix.org/pymix/