PacBio RS SMRT Sequencing Technology: Hybrid Exercises Towards Achieving High Quality de novo Genome Assemblies and Incorporating such Workflows into YABI Environment

The Pacbio^® (Pacific Biosciences) RS is the first third-generation sequencing technology. PacBio SMRT (single molecule real time) technology enables sequencing single DNA molecules in real time. SMRT sequencing advantages include short run time to yield reads of average length over 2,500 base pairs (few reads > 10,000 base pairs) referred to as Continuous Long Reads (CLR), no amplification step resulting in more evenly covered genomes, and apparent absence of GC content bias. A disadvantage of PacBio’s SMRT sequencing approach is the high raw read error rate compared to other sequencing technologies, albeit, there are several computational methods developed to error correct and improve the quality of CLR data. This study compares assemblies from different sequencing platforms and emphasizes the advantages of combining PacBio data with Illumina short reads to obtain better assembly metrics. We present comparative results of Illumina only, PacBio only, and error-corrected hybrid genome assemblies. The results demonstrate error-corrected PacBio RS CLR data provides superior results and helps in generating better genome assemblies. In the course of performing these analyses, we have attempted to formalize and incorporate various multistage bioinformatics protocols into the YABI workflow environment developed at Murdoch University. YABI is user friendly and has the exceptional ability of handling large amounts of data, both raw and processed, by enabling seamless and transparent access to heterogeneous HPC (High Performance Computing) and cloud resources.