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

摘要

Background In recent years, massively parallel complementary DNA sequencing (RNA sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust 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 organisms has been on the rise recently and new tools are frequently developing, there is still a knowledge gap about which assembly software should be used to build a comprehensive de?novo assembly. Results Here, we present a large-scale comparative study in which 10 de?novo assembly tools are applied to 9 RNA-Seq data sets spanning different kingdoms of life. Overall, we built 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. Moreover, we observed species-specific differences in the performance of each assembler. No tool delivered the best results for all data sets. Conclusions 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.