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Thursday, January 31, 2013

Genome Finishing Gets Easier with PacBio Software Update

Plus: Accuracy Boost, Integrated Full-Length cDNA Analysis and Barcoding Support We’re pleased to announce the release of a new software upgrade — SMRT® Analysis v1.4.0 — that achieves higher quality genome assemblies with near-perfect base-level accuracy. You can read documentation, check out data, and download the new software from DevNet. SMRT Analysis v1.4.0 includes a new hierarchical de novo genome assembly process (HGAP), which allows researchers to assemble entire microbial and fungal genomes using just PacBio® long reads. As a result, users can generate better assemblies with a single library preparation and fewer SMRT Cells than previous approaches that also required short-read sequencing…

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Thursday, January 31, 2013

SMRT Sequencing for Industrial Biotech Applications

A feature article in the December 2012 issue of Industrial Biotechnology reports on various case studies where scientists have used the unique capabilities of SMRT® Sequencing to make discoveries in applied biotechnology areas. The long read lengths, high consensus accuracy, lack of sequence bias, and sensitivity to chemical base modifications make SMRT sequencing a good fit for a range of industrial applications, including applied microbiology, agricultural biotechnology, enzyme research and design, pathogen research and detection, biofuels development, and many others.  In an example highlighting the return to the gold standard of high-quality, finished genomes, scientists from the Korea Polar Research…

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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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Thursday, January 17, 2013

SMRT Sequencing Selected by 100K Pathogen Genome Project to Finish Genomes

A recently announced partnership with the University of California, Davis (UC Davis) highlights the benefits of one of the key applications for Single Molecule, Real-Time (SMRT®)  Sequencing: rapid and complete finishing of pathogen genomes. As part of the project, Pacific Biosciences’ SMRT technology will be used for the 100KPathogen Genome Project to sequence the genomes from at least 1,000 foodborne pathogen samples to completion, and to elucidate their epigenomes. These bacteria represent major illness-causing pathogens, including Salmonella, Campylobacter, E. coli, Vibrio, and Listeria. Speaking to GenomeWeb, Bart Weimer, Professor and Director of the 100K Genome Project, commented that building these…

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Monday, January 14, 2013

Baylor Team Uses PacBio’s SMRT® Sequencing to Upgrade and Finish Draft Genomes

Scientists at the Human Genome Sequencing Center at Baylor College of Medicine recently published a paper demonstrating the utility of PacBio’s long reads for upgrading and finishing draft genomes. “Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology,” published in PLoS One late last year from lead author Adam English and senior author Richard Gibbs, details a method for improving draft genomes, many of which have been assembled from short-read sequence data. In addition, the Baylor team has developed its own algorithm called PBJelly to automate the finishing process, optimized for long-read sequence data. According to the…

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Friday, January 11, 2013

PAG 2013 – What Would You Do with a Complete Genome?

We’re pleased to be hosting a workshop at the 21st annual International Plant & Animal Genome conference in San Diego next week — and whether you’re attending or not, we invite you to participate. The workshop will focus on generating high-quality bacterial, plant, and animal genomes using SMRT® Sequencing technology. If you’ll be at PAG, we encourage you to reserve a seat to attend the event. If not, sign up to receive a recording of the workshop. Our event will take place on Tuesday, January 15th from 1:30 to 3:30 p.m. in the San Diego Room. We’ll have presentations from…

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Wednesday, January 9, 2013

Looking Ahead: The 2013 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer With our minds turning to what 2013 has in store for us, it’s a good opportunity to look ahead to the advances you can expect in Single Molecule, Real-Time (SMRT®) Sequencing. We have many improvements coming to the PacBio® RS and we hope you’ll find them as exciting as we do. As many of you know, we released a number of upgrades at the end of 2012 to improve the PacBio RS platform, including a new loading system that reduces the amount of sample required and the new XL chemistry that boosts average read…

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