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. 2015 Jan 27;16(1):29. doi: 10.1186/s12864-015-1221-1

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© Darwish et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), 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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Diagram illustrating two alternative assembly pipelines. (A) De novo assembly and alignment pipeline using Trinity and PASA. (B) Reference guided assembly pipeline using TopHat and Cufflinks.