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http://compbio.cs.brown.edu/software

README for PREGO (Paired-End Reconstruction of Cancer Genome Organization)

Software that reconstructs a cancer genome as a rearrangement of segments, 
or intervals, from the reference genome using paired end sequencing data.

If you use this software in your research, please cite:

L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, B.J. Raphael. (2012) 
Reconstructing cancer genomes from paired-end sequencing data. 
BMC Bioinformatics (Proceedings of 2nd Annual RECOMB Satellite 
Workshop on Massively Parallel Sequencing (RECOMB-seq)). 
13(Suppl 6):S10.

Corresponding Authors:
Layla Oesper (layla@cs.brown.edu)
Ben Raphael (braphael@cs.brown.edu)

Version: 1.1
Version Date: May 22, 2013

SUMMARY ==========================================================

This README file lists and annotates the files distributed with the
Version 1.1 release of the software for the PREGO algorithm.

CONTENTS ========================================================

(i) Documentation (in doc/ subdirectory ):
* Manual; MANUAL.txt - A complete description of how to install/run the software.

(ii) Software (in java/src/ subdirectory ):
* Source code in java/src

(iii) Executables (in bin/ subdirectory ):
* Exectutables for compiling and running code

(iv) Example (in example/ subdirectory ):
* Example input files: example.intervalEdges, example.variantEdges