TOA-Manuscript-Performance-Evaluation-Tests

Table of contents

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".

Directories:

benchmark-transcriptomes: Fasta files with the sequences corresponding to the benchmark transcriptomes tested in the manuscript:

            Cnuc: Cocos nucifera embryos (Huang et al., 2014).

            Fsyl: Fagus sylvatica leaves (Müller, Seifert, Lübbe, Leuschner, & Finkeldey, 2017).

            Pcan: Pinus canariensis immature xylem (Chano, Collada, & Soto, 2017).

TOA: output of the six simulation tests performed with TOA.

EnTAP: output of the six simulation tests performed with EnTAP.

Trinotate: output of the three simulation tests performed with Trinotate.

References:

Chano, V., Collada, C., & Soto, A. (2017). Transcriptomic analysis of wound xylem formation in Pinus canariensis. BMC Plant Biology, 17(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., & Matzke, M. (2014). De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. G3: Genes, Genomes, Genetics, 4(11), 2147–2157. doi:10.1534/g3.114.013409

Müller, M., Seifert, S., Lübbe, T., Leuschner, C., & Finkeldey, R. (2017). De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. PLoS ONE, 12(9), 1–20. doi:10.1371/journal.pone.0184167