Michael Schatz, Ph.D. Assistant Professor of Quantitative Biology at Cold Spring Harbor Laboratory, shares some thoughts about his experience with the PacBio RS and his hopes for future work with the new PacBio RS II:
“For several important genomic analysis, including de novo genome assembly, mapping structural variations, and discovering alternative splicing, we are principally limited by the read lengths of sequencing technology available. When it comes to assembling a genome, for example, read length is critically important for spanning repetitive sequences, as reads shorter than those repeats fundamentally just don’t have enough information for the assembler to determine the correct structure. With structural variations, such as copy number changes, long reads are needed to correctly characterize the flanking sequences. With alternative splicing, long reads let us analyze entire transcripts at once, avoiding the complicated inference of isoforms.
As such, I’m extremely interested in the long read capabilities of the PacBio RS and now the RS II. My lab has been involved in a number of projects where the read lengths produced by the RS, some exceeding 20 kbp long, were the keys to unlocking the underlying biology, which was impossible to determine using alternate short read technologies.
We are fast approaching the day where assembling bacterial chromosomes into individual contigs with the RS is routine, and if the RS II can deliver as expected, it is quite likely we will soon see this capability transfer to larger eukaroytic genomes. Already with the RS, the contigs from our de novo assembly of the 400Mbp rice genome are several fold better than the state-of-the-art ALLPATHS-LG assembly using short reads. I’m very excited and optimistic to see how far we can push genome assembly in this and other organisms with the RS II later this year.”
See Dr. Schatz’s most recent presentation given at the University of Virginia, entitled “De novo assembly of complex genomes.”