Benchmarking Alignment and Quantification Tools on Plant RNA-Seq Data with CyVerse Cyberinfrastructure

RNA-seq has become a workhorse in transcriptomic studies. This is primarily because improvement in sequencing technology over the years has made it more affordable to perform full transcriptomic experiments with deeper coverage as compared to initial days of RNA sequencing. As a result, this has manifested in a data deluge from RNA-seq experiments. The current ecosystem of RNA-seq tools have more efficient and scalable options, with inclusion of tools like HISAT2, StringTie and Ballgown as alternates to the existing Tuxedo protocol that has been the preferred suite of tools used for RNA-seq analysis.There is also emergence of other pseudo-alignment based RNA-seq tools, such as Kallisto, Sailfish and Salmon, which serve as alternates to the existing aligners. Most tools have been benchmarked for scalability and sensitivity using human datasets. In this study, we will be focusing on benchmarking plant dataset with new and existing tools integrated into CyVerse Discovery Environment. In addition, we will leverage epigenetic data for evaluating accuracy of different tools. In summary, we will benchmark these tools for both accuracy and speed, thus provide a guideline for using them on plant RNA-seq studies.