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ARDEN - Artificial Reference Driven Estimation of false positives in NGS
https://sourceforge.net/p/arden/

CURRENT VERSION: 1.0

---------------------------------------------------------------------------
Table of Contents
---------------------------------------------------------------------------
  1.   	Overview
  2.  	Latest Version
  3.  	Documentation
  4.   	Installation
  5.   	Dependencies
  6.	Usage Example
  7.	Contact
  8. 	Licensing
  
  
 1. Overview 
 ---------------------------------------------------------------------------
 ARDEN is a collection of tools to estimate the number of false positives in NGS 
 read mapping. It includes three moduls ('createAR','analyse' and 'filter') to 
 perform a False Discovery Rate estimation. For a detailed getting started guide
 have a look at the wikki:
	https://sourceforge.net/p/arden/
 
 
  
 2. Latest Version 
 ---------------------------------------------------------------------------
  The latest version of ARDEN can be downloaded at sourceforge:
  The current version is 1.0
	https://sourceforge.net/p/arden/
 
 
  3. Documentation
 ---------------------------------------------------------------------------
  The documentation is available as of the date of this release in html format 
  in the docs/ directory. You may also find useful information in the wikki:
	https://sourceforge.net/p/arden/
 
 
  4. Installation 
 ---------------------------------------------------------------------------
 ARDEN is a collection of python scripts and therefore needs no installation.
 It was built and tested on a Linux platform. However, for convenient access it
 is recommended to do the following adjustments to your environment variables:
	export PATH = $PATH:/path/to/ARDEN
	
	
  5. Dependencies 
 ---------------------------------------------------------------------------
 ARDEN makes use of the following python packages, that are all mandatory
 (ARDEN was developed under Python 2.7):
 
	* Python 2.7, http://www.python.org/
	* NumPy 1.6.1, http://numpy.scipy.org/
	* SciPy 0.10.0, http://www.scipy.org/
	* HTSeq 0.5.3p9,	 https://pypi.python.org/pypi/HTSeq
	* matplotlib 1.1.0,	 http://matplotlib.org/
	
 
   6. Usage Examples 
 ---------------------------------------------------------------------------
  ARDEN consists of various programs:
	* arden-create:		creates an artificial reference genome for a given DNA sequence
	* arden-analyse:	compares results on the artificial and original reference mappings
	* arden-filter:		depending on a user defined cut-off a SAM file is filtered
	
 To display the detailed help information for every tool just run arden-toolname --help, 
 e.g. arden-create --help. For a getting started guide visit the wikki on sourceforge.net
 
   6.1 arden-create 
 ---------------------------------------------------------------------------
  The aim is to generate an artificial reference genome from an input genome. 
  The target folder have to specified as 1st argument. There are various options
  constraining this task. The most important option is the minimum distance between
  two subsitutions. It is specified with -d and should be adjusted to read length
  and desired error level. The final value for is internally d-3. If you specify
  -d 15 as option the minimum distance will be 12.
  
	arden-create results/ sample.fasta -d 18
	

   6.2 arden-analyze 
 ---------------------------------------------------------------------------
  The aim is to compare mappings (in sorted SAM file format) of the reference genome
  and the artificial genome created in the first step. Since a lot of input options
  are required the program is controled through an inifile. Refere to doc\sample\ 
  or the online wikki for creating this file correctly.

  In general the ini file looks like this (with 2 mapper specified):
  
  	$:/PATH/TO/REFERENCE/FASTA
	#:/PATH/TO/ARTIFICIAL/FASTA
	&:/PATH/TO/READFILE
	@MapperName_1
	ref:PATH/TO/SORTED/SAM/FILE/REFERENCE_1
	art:PATH/TO/SORTED/SAM/FILE/ARTIFICIAL_1
	+	
	@MapperName_2
	ref:PATH/TO/SORTED/SAM/FILE/REFERENCE_2
	art:PATH/TO/SORTED/SAM/FILE/ARTIFICIAL_2
	+
	
	
	arden-analyze inifile.txt outputfolder/
	
 

   6.1 arden-filter 
 ---------------------------------------------------------------------------
  Given a sensitivity and specificity analyzes and the corresponding alignment
  features a new SAM file is generated, where suboptimal alignments are excluded.
  The options are the read quality score , number of gaps, number of mismatches,
  the alignment file in sorted SAM format and the desired outputfilename.
  The relation concerning the options are the following: rqs >= option, 
  gaps <= option, mismatches <= option.
  
	arden-filter alignment.sam filtered.sam -r 0 -g 3 -m 3
	
	
	
  8.	Contact
   ---------------------------------------------------------------------------
 	For any suggestions please contact renardB@rki.de.
 
  9.	Licensing
  ---------------------------------------------------------------------------
   
   	Copyright (c) 2012, Sven H. Giese, gieseS@rki.de, 
	Robert Koch-Institut, Germany,
	All rights reserved.
	
	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions are met:
	    * Redistributions of source code must retain the above copyright
	      notice, this list of conditions and the following disclaimer.
	    * Redistributions in binary form must reproduce the above copyright
	      notice, this list of conditions and the following disclaimer in the
	      documentation and/or other materials provided with the distribution.
	    * The name of the author may not be used to endorse or promote products
	      derived from this software without specific prior written permission.
	
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
	ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
	WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	DISCLAIMED. IN NO EVENT SHALL MARTIN S. LINDNER BE LIABLE FOR ANY
	DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
	ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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