July 29, 2013  |  Products, procedures + protocols

As Cores Upgrade to PacBio RS II, Users Report Data and Progress

As PacBio customers are upgrading to the new PacBio® RS II System, some of our core lab users have already begun blogging about the improved results.

At the University of Maryland’s Institute for Genome Sciences (IGS), for example, one blogger posted data comparing read length, read count, and throughput for the PacBio RS and PacBio RS II. The post reports a comparison of an 8 Kb Mycobacterium project run on the PacBio RS and again on the PacBio RS II, finding that with the upgrade, “we see an almost 3x increase in total yield [per SMRT Cell], while read lengths remain about the same.”

Be sure to check out the blog post, which includes several charts showing different ways to visualize the data generated by both instruments. The blog post concludes, “Although we are early in our use and optimization of the new PacBio RS II, we are encouraged by the increase in both yield and read length, and expect continued improvement in our PacBio data, subsequently improving data analysis and genome assembly.”

For another user’s experience, don’t miss Lex Nederbragt’s blog post about incorporating the PacBio RS II upgrade at the Norwegian Sequencing Centre (NSC) at the University of Oslo. “We have never seen such long reads,” Nederbragt writes, offering several charts with data on read length and throughput from four bacterial libraries. The blog post also details the rest of the process, using HGAP, Quiver, and Celera® Assembler to pull the sequence into mostly one large contig for each genome.

For more from these bloggers, check out:
– An IGS blog post reporting data from using HGAP in a genome assembly pipeline
– A blog post about optimizing read length by adding the BluePippin™ system to the PacBio workflow at NSC

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