README

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Pollux
Copyright (C) 2014-2015 Eric Marinier

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

======================================================================

-- Description --

Pollux is a platform independent error corrector which targets errors 
produced by second-generation sequencing technologies.

-- Release --

Pollux 1.0.2
6 June 2015

Fixed a crash when the output directory was missing.

-- Requirements --

Pollux requires a 64 bit Unix-based operating system.

-- Installation --

make

-- Running Pollux --

Pollux's command line arguments can be found by running:
./pollux

Simple correction:
./pollux -i <fastq_reads>

Paired correction:
./pollux -p -i <fastq_reads_1> <fastq_reads_2> -o ouput

-- Contact --

Brendan McConkey: mcconkey@uwaterloo.ca
Eric Marinier: eric.marinier@phac-aspc.gc.ca

-- Publication --

Marinier, Eric, Daniel G. Brown, and Brendan J. McConkey. 
"Pollux: platform independent error correction of single and mixed genomes."
BMC Bioinformatics 16.1 (2015): 10.

-- Credits --

The Makefile is derived from yanick.rochon@gmail.com (2010-11-05).
(http://stackoverflow.com/users/320700/yanick-rochon)

The source makes use of data structures provided by Simon Howard.
(http://c-algorithms.sourceforge.net/)