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. 2016 Jul 11;5:30. doi: 10.1186/s13742-016-0135-4

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© The Author(s). 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Example of a command line script. This script can be used to align DNA sequence data to a reference genome. First, it downloads the software and data files necessary for the analysis. Then, it extracts (“unzips”) these files, and aligns the data to a reference genome for Ebola virus. Finally, it converts, sorts, and indexes the aligned data. See Additional file 1 for an executable version of this script