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. 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