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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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Wednesday, July 3, 2013

Genome Biology Commentary Discusses the Advantages of SMRT Sequencing

A new commentary in Genome Biology from highly respected scientific authors, including a Nobel Prize winner, highlights the benefits of Single Molecule, Real-Time (SMRT®) Sequencing.  The commentary, entitled “The advantages of SMRT sequencing,” comes from Richard Roberts at New England BioLabs, Mauricio Carneiro at the Broad Institute, and Michael Schatz at Cold Spring Harbor Laboratory. The authors begin with the premise that the PacBio® RS is sometimes overlooked as a next-generation sequencing option, even though it serves as “ideal approach to the complete sequencing of small genomes.” The commentary focuses on three advantages of SMRT Sequencing: extraordinarily long reads, methylation…

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Tuesday, June 18, 2013

Back from SFAF, and Eager for More Finished Genomes

Last month’s Sequencing, Finishing, Analysis in the Future  (SFAF) meeting in Santa Fe, New Mexico, hosted by Los Alamos National Laboratory, attracted terrific scientists and we really enjoyed hearing about their work as well as sharing our own technology advances. It was great to be at a meeting where genome finishing and analysis were key themes; it was an environment where our customers’ experience with HGAP and Quiver resonated, particularly around the automated finishing of microbial genomes. SFAF had a number of keynote speakers, including Mark Adams from the J. Craig Venter Institute, who spoke about antibiotic resistance in microbes.…

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Friday, June 14, 2013

Two Worlds of Genome Assemblers

by Jonas Korlach, Chief Scientific Officer Finished genomes were the focus of last month’s Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico. In addition to several presentations, including a talk by Adam Phillippy from the National Biodefense Analysis and Countermeasures Center that demonstrated the ability to generate high-quality, finished microbial genomes using just long-read PacBio data, several papers have appeared recently describing the same principle: the HGAP/Quiver Nature Methods paper, the FDA’s Salmonella Javiana outbreak genome publication, a blog entry by the University of Maryland using HGAP, and a preprint by Adam Phillippy and colleagues…

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Tuesday, May 14, 2013

Nature Methods Paper Demonstrates a Cost-Effective Process for Finishing Genomes

A paper recently published in Nature Methods offers a deep dive into the use of our HGAP and Quiver tools to generate a high-quality genome assembly with an automated, simplified workflow. (“Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data,” Chin et al., advance online publication.) The publication, which includes lead author Chen-Shan Chin and others at Pacific Biosciences as well as collaborators at the Joint Genome Institute and the Eichler lab at the University of Washington, uses Single Molecule, Real-Time (SMRT®) Sequencing on three microorganisms and one human BAC to compare PacBio-only sequencing to existing high-quality reference genomes.…

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Thursday, February 14, 2013

Mendelspod Interview with Mike Hunkapiller, CEO of Pacific Biosciences

Mike Hunkapiller was interviewed for a podcast recently on Mendelspod. In it, Mike and Mendelspod host Theral Timpson chat about the current sequencing technology landscape, clinical applications of sequencing, and Mike’s goals as the head of PacBio.     Here are a few highlights from the interview: On the need for de novo sequencing of microbes rather than relying on reference assemblies: “[Their] genomes are evolving so fast because they can pick up genes from other organisms really easily — you almost by definition don’t have good references.” On SMRT® Sequencing accuracy: “We have the highest accuracy in the field, but…

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Tuesday, January 22, 2013

A Closer Look at Accuracy in PacBio Sequencing

By Jonas Korlach, Chief Scientific Officer Single Molecule, Real-Time (SMRT®) DNA sequencing achieves highly accurate sequencing results, exceeding 99.999% (Q50) accuracy, regardless of the DNA’s sequence context or GC content. This is possible because SMRT sequencing excels in all three categories that are relevant when considering accuracy in DNA sequencing: 1.      Consensus accuracy 2.      Sequence context bias 3.      Mappability of sequence reads Since there has been some confusion in the community about accuracy in SMRT sequencing, I would like to describe how our system performs and how such high accuracy is achieved. You can download the full perspective, complete with…

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