TOA-Manuscript-Performance-Evaluation-Tests

<strong>Table of contents</strong> This repository contains the data that support the findings of the manuscript "TOA: a software package for automated functional annotation in non-model plant species". <strong>Directories:</strong> <strong>benchmark-transcriptomes:</strong> Fasta files with the sequences corresponding to the benchmark transcriptomes tested in the manuscript: <strong>Cnuc:</strong> <em>Cocos nucifera</em> embryos (Huang et al., 2014). <strong>Fsyl:</strong> <em>Fagus sylvatica</em> leaves (Müller, Seifert, Lübbe, Leuschner, &amp; Finkeldey, 2017). <strong>Pcan:</strong> <em>Pinus canariensis</em> immature xylem (Chano, Collada, &amp; Soto, 2017). <strong>TOA:</strong> output of the six simulation tests performed with TOA. <strong>EnTAP:</strong> output of the six simulation tests performed with EnTAP. <strong>Trinotate:</strong> output of the three simulation tests performed with Trinotate. <strong>References:</strong> Chano, V., Collada, C., &amp; Soto, A. (2017). Transcriptomic analysis of wound xylem formation in <em>Pinus canariensis</em>. <em>BMC Plant Biology</em>, <em>17</em>(234). doi:10.1186/s12870-017-1183-3 Huang, Y. Y., Lee, C. P., Fu, J. L., Chang, B. C. H., Matzke, A. J. M., &amp; Matzke, M. (2014). <em>De novo</em> transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. <em>G3: Genes, Genomes, Genetics</em>, <em>4</em>(11), 2147–2157. doi:10.1534/g3.114.013409 Müller, M., Seifert, S., Lübbe, T., Leuschner, C., &amp; Finkeldey, R. (2017). <em>De novo</em> transcriptome assembly and analysis of differential gene expression in response to drought in European beech. <em>PLoS ONE</em>, <em>12</em>(9), 1–20. doi:10.1371/journal.pone.0184167