Improving Genomes Using Long Reads and PBJelly 2

High quality reference genome sequences are the foundation of genetic analyses.  The thousands of gaps remaining in even “high quality” draft genome sequences adversely impact the assessment of genes and other functional elements.  With the long reads provided by Pacific Bioscience’s PacBios RS technology and our first generation PBJelly software we upgraded several draft genomes, including new de novo genomes assembled with Illumina short read data, Roche 454 and Sanger sequences.  Our latest PBJelly 2 software leverages the current SMRT analysis pipeline and adds scaffolding to fill inter-scaffold gaps as well as the intra-scaffold gaps addressed by PBJelly 1.  Other improvements increased the accuracy of the gap-filling sequence.   Our results applying the PBJelly 2 to existing data sets as well as to even longer read sets produced with the latest Pacific Biosciences sequencing polymerase and chemistry will be presented.