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Thursday, August 22, 2013

The Value of Finished Bacterial Genomes: A Microbiology Primer

Microbiologists have been at the forefront of genomics since Haemophilus influenzae became the first organism to have its full genome sequenced in 1995 using Sanger sequencing. Even with modern technology, we are just beginning to appreciate the complex interactions between microbes and Earth’s many ecosystems. For example, the human body is composed of ten times as many bacterial cells as human cells, helping us to process food, moderating our immune system, and protecting us from the environment. The growing awareness of the critical role microorganisms play in our lives has led to increasing efforts to understand them. It is becoming…

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Monday, July 22, 2013

New Genomes for 100K Pathogen Project Sequenced and Finished with PacBio Technology

The 100K Foodborne Pathogen Genome Project announced the contribution of 20 newly finished genomes of microbes responsible for foodborne disease, and we’re pleased to report that they were sequenced and assembled using automated PacBio® pipelines. The 100K Genome Project aims to sequence the genomes of 100,000 bacterial and viral genomes with the goal of speeding up the diagnosis and treatment of foodborne diseases and shortening the outbreak time. The global effort is led by the University of California, Davis, the Center for Food Safety and Applied Nutrition of the US Food and Drug Administration, and Agilent Technologies; Pacific Biosciences is…

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Wednesday, July 10, 2013

University of Oslo Scientists Use Long Reads for Unique Look at Cod Genome

Scientists at the University of Oslo’s Centre for Ecological and Evolutionary Synthesis (CEES) have used multi-kilobase sequence reads from the PacBio® RS sequencer to produce a dramatically improved genome assembly for the Atlantic cod.  In many ways the cod genome seemed like a puzzle that might never be fully solved, but the Single Molecule, Real-Time (SMRT®) Sequencing platform made significant inroads — and just in time, as the team of researchers working on cod recently received funding to resequence 1,000 more of them. Being able to base these new efforts on a reliable genome assembly will make future results far…

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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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Thursday, April 18, 2013

Guest Blog: Michael Schatz shares his perspective on the new PacBio RS II

Michael Schatz, Ph.D. Assistant Professor of Quantitative Biology at Cold Spring Harbor Laboratory, shares some thoughts about his experience with the PacBio RS and his hopes for future work with the new PacBio RS II: “For several important genomic analysis, including de novo genome assembly, mapping structural variations, and discovering alternative splicing, we are principally limited by the read lengths of sequencing technology available. When it comes to assembling a genome, for example, read length is critically important for spanning repetitive sequences, as reads shorter than those repeats fundamentally just don’t have enough information for the assembler to determine the…

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Wednesday, April 10, 2013

Rapid Genome Assembly: Salmonella Outbreak Strain Sequenced and Closed in Less Than One Week

A newly reported Salmonella genome showcases the utility of single molecule, real-time (SMRT®) sequencing for characterizing a foodborne outbreak pathogen. The outbreak strain, Salmonella enterica subsp. enterica serovar Javiana (S. Javiana), representing one of the top five most common forms of Salmonella associated with fresh-cut produce, was sequenced and analyzed late last year; its genome was published this month in Genome Announcements, a journal from the American Society for Microbiology. The study was led by the US Food & Drug Administration’s Center for Food Safety & Applied Nutrition. Scientists from Pacific Biosciences and New England BioLabs participated in the study,…

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Tuesday, April 9, 2013

It’s a Very Microbial Season

This springtime, we’ve got microbes on the brain! The annual meeting of the American Society for Microbiology is just over a month away, so we’ve been thinking a lot about microbial genomics and how we can contribute to this burgeoning field. Microbiology is a key application for customers using the PacBio® RS. With its throughput, turnaround time, cost-effectiveness, and long reads, it is the perfect tool for performing de novo sequencing of microbes and generating closed genomes — often bringing microbial genomes together in a single contig. Beyond that, the unique way in which SMRT® Sequencing produces epigenetic data together…

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Thursday, March 7, 2013

From In Sequence: Spotlight on PacBio Customers’ Data at AGBT 2013

A recent article from In Sequence highlights several of our customers and the great projects they’ve been working on with single molecule, real-time (SMRT®) sequencing. If you’re not a subscriber to the newsletter, you can access the story here. In the article, GenomeWeb’s Monica Heger reports on several PacBio customer talks from the Advances in Genome Biology & Technology meeting, including presentations from Eric Antoniou and Mike Schatz at Cold Spring Harbor, and Eric Schadt at Mt. Sinai. The article also reports on a talk given by our CSO, Jonas Korlach. According to the article, “Pacific Biosciences and several users recently…

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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 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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