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README
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README
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DOCUMENTATION
-------------
https://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.
https://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
* https://cam.cornell.edu
* AND
* Rob Egan
* Department of Energy Joint Genome Institute
* https://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
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS WITH THE SOFTWARE.
*/
// For more information on the licence please see
// The University of Illinois/NCSA Open Source License
// https://www.opensource.org/licenses/UoI-NCSA.php
INSTALL
-------
https://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 https://www.pymix.org/pymix/