1. Instruction Manual
Authors: D. J. Edwards, B. J. Pope and K. E. Holt
Date: Sept 7, 2016
NOTE: most up-to-date manual available in 'docs' folder as a PDF
Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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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.
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Neither the name of the copyright holder nor the names of its contributors may 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 THE COPYRIGHT HOLDER OR CONTRIBUTORS 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.
Edwards, D. J., Pope, B. J., and Holt, K. E. (2015) RedDog: comparative analysis pipeline for large numbers of bacterial isolates using high-throughput sequences. In prep. (working title only)
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Obtaining the Current Version of RedDog
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Reporting a Problem with RedDog
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RedDog Dependencies
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Using RedDog on a Dedicated Server
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Running the Pipeline
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Pipeline Conventions
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Pipeline Test Sets
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Configuration File
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Essential Pipeline Variables
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Other Pipeline Variables
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Advanced Settings
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Rubra pipeline variables
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Large Data Sets, Large Read Sets and High Variation
- [Large Data Sets] (https://github.com/katholt/RedDog/wiki/8.-Advanced-Settings#large-data-sets)
- [Large Read Sets] (https://github.com/katholt/RedDog/wiki/8.-Advanced-Settings#large-read-sets)
- [High Variation] (https://github.com/katholt/RedDog/wiki/8.-Advanced-Settings#high-variation)
- [Summary Table] (https://github.com/katholt/RedDog/wiki/8.-Advanced-Settings#summary-table---large-data-sets-large-read-sets-and-high-variation)
- [Large Data Sets] (https://github.com/katholt/RedDog/wiki/8.-Advanced-Settings#large-data-sets)
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Rubra pipeline variables
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Clean-up
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Pipeline Outputs
- [Further Analysis: parseSNPTable] (https://github.com/katholt/RedDog/wiki/11.-Further-Analysis:-parseSNPTable)
- [Troubleshooting a Pipeline Run] (https://github.com/katholt/RedDog/wiki/12.-Troubleshooting-a-Pipeline-Run)
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Details - Current Version
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Details - Previous Versions
- Example Flowchart
- Understanding the Output