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. 2014 May 23;7:314. doi: 10.1186/1756-0500-7-314

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Copyright © 2014 Onsongo et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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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Flowchart for analysis pipeline. A metadata file describing the sequence data being uploaded for analysis together with the location of the files are passed as input to a shell script. The shell script configures the VM on Amazons AWS and uploads data to the VM. A Galaxy workflow is used for Phase 1 of the analysis. QC results are examined to verify data meets quality thresholds. A second Galaxy workflow is used for Phase 2 of the analyses producing a VCF file containing variants.