PacBio Upgrades Increases Average Read Length to 5000 Bases

PacBio Upgrades to produce 5000 bp reads

PacBio Upgrades to produce 5000 bp reads

Just a few hours ahead of ASHG Annual Meeting at San Francisco (ASHG12), Pacific Biosciences announced improvements to its sequencing system, that will enable PacBio RS to sequence longer reads. The new upgrades to DNA Sequencing Chemistry and Software increases PacBio RS’s average read length from 3,000 bases to 5,000 bases and the reads can be as long as 20,000 bases.

In its press release, giving more details on the improvement, PacBio highlighted three features that helped PacBio to produce longer reads. The longer read length is partly due to new faster polymerase that reads more bases per second in the new chemistry.

And the upgrade also includes a new feature called “Stage Start feature”, which enables sequence data collection to begin as soon as the polymerase is activated and producing longer reads. In addition, the upgrade also lets the PacBio system to record data during the sequencing reaction for a longer period, thus increasing the read lengths.

Dr. Jonas Korlach, Chief Scientific Officer of Pacific Biosciences, said

The XL release is an enhancement to our existing C2 chemistry to address applications that require the longest reads, like de novo assembly. A unique characteristic of our SMRT sequencing technology is the ability to tune the experimental design to maximize results for the project’s application and goals. Through this flexibility and our continued performance enhancements, our customers can carry out their current research projects more efficiently, and engage in new applications to help resolve very complex genomes and transcriptomes.

PacBio’s Dr. Korlach will talk about the latest upgrade in a workshop at the ASHG meeting that begins today at San Francisco. Commenting on the use of longer Pacbio reads in assembling the complex rice genome, Dr. Mike Schatz from Cold Spring Harbor labs said,

Adding the long reads from PacBio doubled the contig connectivity over the current state-of-the-art ALLPATHS-LG assembler and mate-pair recommendations.

With the new chemistry, the CSHL team could assemble rice genome with 9x coverage with 50% of the data coming from reads longer than 4,800 base pairs.

Pacific Biosciences launched its Single Molecule Real Time (SMRT) DNA Sequencing System in Feb, 2010 as part of its early access program. PacBio RS can produce longer reads than its current competitors. However, PacBio has been finding it tough to make inroads into sequencing market, given its high cost ( about $700,000) and high error rates.

PacBio reads have 16% – 20% error rate and the error rate increases to 16%-20% immediately with in 100-200 bases and stays constant up to its full read length. On the market front, PacBio said in its latest quarterly financial results, the company has posted $2.8 million in revenue, suggesting that it probably sold just 4-5 units of PacBio RS.


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