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Quality of RNA-Seq Toolset
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README.md

QoRTs v1.3.6

(Compiled Tue Sep 25 11:21:46 EDT 2018)

The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Its primary function is to aid in the detection and identification of errors, biases, and artifacts produced by high-throughput sequencing technology. In addition, it can produce count data designed for use with RNA-Seq differential gene expression and differential exon usage tools, as well as individual-sample and/or group-summary genome track files suitable for use with the UCSC genome browser (or similar browsers). The entire QoRTs toolkit can be used in almost any operating system that supports java and R. For more information visit the QoRTs project page.

##Citing QoRTs: If you use QoRTs and find it helpful, you can cite it in your publications as:

Hartley SW, Mullikin JC. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. BMC Bioinformatics. doi: 10.1186/s12859-015-0670-5

##HELP AND DOCUMENTATION: Additional help and documentation is available online here.

If you have a question, encounter an error, or have a feature request, we recommend that you create an issue on the github issues page.

Alternatively, the creator and maintainer of QoRTs can be reached by emailing "QoRTs-contact" (at) list.nih.gov.

##LEGAL: This software is "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors’ official duties for the United States Government and thus QoRT Package User Manual cannot be copyrighted. This software is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose.

In any work or product derived from this material, proper attribution of the authors as the source of the software or data should be made, using "NHGRI Genome Technology Branch" as the citation.

The QoRTs Scala package includes (internally) the sam-JDK library (sam-1.113.jar) from picard tools, which is licensed under the MIT license: The MIT License Copyright (c) 2009 The Broad Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 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 AUTHORS 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 IN THE SOFTWARE.

The MIT license and copyright information can also be accessed using the command: \begin{framed} \begin{verbatim} java -jar /path/to/jarfile/QoRTs.jar "?" samjdkinfo \end{verbatim} \end{framed}

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