Supporting data for "De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers"

In recent years, massively parallel cDNA sequencing (RNA-Seq) has emerged as a fast, cost-effective and powerful technology to study entire transcriptomes in various manners. In particular, for non-model organisms and in the absence of an appropriate reference genome, RNA-Seq is used to reconstruct the transcriptome de novo. Although the de novo transcriptome assembly of non-model organism has been on the rise recently and new tools are developed frequently, there is still a knowledge gap about which assembly software should be used to build a comprehensive de novo assembly. Here we present a large-scale comparative study in which ten de novo assembly tools are applied to nine RNA-Seq data sets spanning different kingdoms of life. Overall, we build more than 200 single assemblies and evaluated their performance on a combination of 20 biological-based and reference-free metrics. Our study is accompanied by a comprehensive and extensible Electronic Supplement that summarizes all data sets, assembly execution instructions, and evaluation results. Trinity, SPAdes and Trans-ABySS, followed by Bridger and SOAPdenovo-Trans, generally outperformed the other tools compared. In addition, we observed species-specific differences in the performance of each assembler. No tool delivered the best results for all data sets. We recommend a careful choice and normalization of evaluation metrics to select the best assembling results as a critical step in the reconstruction of a comprehensive de novo transcriptome assembly.