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. 2014 Mar 12;15(1):188. doi: 10.1186/1471-2164-15-188

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© Melicher et al.; licensee BioMed Central Ltd. 2014

This article is published under license to 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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Frequency distribution of transcript lengths by assembly. A plot of the quantity of transcripts with a given length per assembly shows differences in assembly output and a pronounced peak representing the median transcript length. The meta-assembly was generated by the re-assembly of all k-mer lengths using CAP3. Meta-assembly improved transcript length, as indicated by the leading edge of the graph. Meta-assembly also reduced the number of short contigs, compared to the single k-mer assemblies. Trinity automatically removes contigs smaller than 200 base pairs.