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. 2015 Sep 29;16:734. doi: 10.1186/s12864-015-1911-8

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© Shelton et al. 2015

Open Access This 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. 2 — Assembly workflow for assemble_SGE_cluster.pl. a The Irys instrument produces tiff files that are converted into BNX text files. b One BNX file is produced for each flowcell on a IrysChip. c BNX files are split by scan and aligned to the sequence reference. Stretch (bases per pixel) is recalculated for each scan from the alignment. d Quality check graphs are created for each pre-adjusted flowcell BNX. e Adjusted flowcell BNXs are merged. f The first assemblies are run with a variety of p-value thresholds. g The best first assembly (red oval) is chosen and a version of this assembly is produced with a variety of minimum molecule length filters