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Wednesday, August 6, 2014

Plant and Animal Genomes: New Web Resource Available

After so many compelling customer projects for microbial genomes, it’s been rewarding to see more scientists turning to Single Molecule, Real-Time (SMRT®) Sequencing for larger genomes, such as plants and animals. Many PacBio users are performing de novo sequencing and assembly or upgrading draft genomes initially generated by short-read technologies. Extraordinarily long reads and throughput improvements have allowed scientists to affordably assemble and close genomes such as the Atlantic cod, spinach, and Orpinomyces, an anaerobic fungus found in the rumen of cows, to name a few. As reported by several customers at the 2014 Plant & Animal Genome conference in…

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Tuesday, July 22, 2014

At ISMB, Gene Myers’ Keynote Offers History, Future of Genome Assembly

At ISMB 2014 in Boston earlier this month, Gene Myers of the Max-Planck Institute for Molecular Cell Biology and Genetics, presented a keynote address entitled “DNA Assembly: Past, Present, and Future.”  Myers received the prestigious Senior Scientist Accomplishment Award from the International Society for Computational Biology (ISCB) at the event. The ISCB Senior Scientist Accomplishment Award honors respected leaders in computational biology and bioinformatics for their significant contributions to these fields through research, education, and service. Myers is being honored as the 2014 winner for his outstanding contributions to the bioinformatics community, particularly for his work on sequence comparison algorithms,…

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Friday, July 11, 2014

ISMB 2014: The World Cup of Bioinformatics

We’re eager for the #ISMB conference — it’s the 22nd annual Intelligent Systems for Molecular Biology event — kicking off this weekend in Boston. As we continue to push our technology to deliver longer read lengths, we have been honored to work with many leading bioinformaticians to optimize the processing and analysis of our data. Several of those experts will be speaking at ISMB this year. On Sunday, attendees will hear from Adam Phillippy of the National Biodefense Analysis and Countermeasures Center. He’ll be presenting at noon on producing complete genome assemblies using Single Molecule, Real-Time (SMRT®) Sequencing data. Adam’s…

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Wednesday, July 9, 2014

Optimizing Eukaryotic De Novo Genome Assembly: Webinar Recording Available

Our webinar on eukaryotic genome assembly attracted a great crowd, and now we’re making the full recording available to the community. The session featured great hands-on information and best practices for working with Single Molecule, Real-Time (SMRT®) Sequencing data. “Optimizing Eukaryotic Genome Assembly with Long-Read Sequencing” featured three excellent speakers — Michael Schatz and James Gurtowski from Cold Spring Harbor Laboratory and Sergey Koren from the National Biodefense Analysis and Countermeasures Center — and was hosted by our own CSO Jonas Korlach. Schatz kicked off the session with an overview of assemblers for PacBio® data (as well as recommendations for…

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Wednesday, May 28, 2014

The Sequence Analysis Meeting: SFAF 2014

The Sequencing, Finishing, and Analysis in the Future (SFAF) meeting kicks off today in Santa Fe, New Mexico. The conference is hosted by Los Alamos National Laboratory and focuses on the analytical details that are so important as the community assesses how to get the most out of all this sequence data. This year, we will have two PacBio speakers, and there will be a number of other talks from users of our long-read sequence data. Steve Turner, our CTO, will speak on Wednesday morning about the use of Single Molecule, Real-Time (SMRT®) Sequencing for generating highly contiguous genome assemblies…

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Thursday, May 22, 2014

At ASM, Pioneering Scientists Presented Bacterial Methylome Highlights

This week’s annual meeting of the American Society for Microbiology was every bit as interesting, data-rich, and jam-packed as promised. We’re grateful to everyone who stopped by our booth and got to know more about Single Molecule, Real-Time (SMRT®) Sequencing. Our favorite session, “Bacterial Methylomes,” took place on the last day of the conference and was organized by Rich Roberts, Nobel laureate and Chief Scientific Officer at New England Biolabs. The session highlighted several projects analyzing genome-wide methylation states of bacteria, a task which has been all but impossible due to the technical inability to detect such base modifications. As…

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Wednesday, April 16, 2014

Innovation Centre in Quebec Uses SMRT Sequencing for
Cost-Effective, Complete Microbial Genomes

At the McGill University and Génome Québec Innovation Centre, many projects conducted in the sequencing core facility fall under the umbrella of life sciences rather than biomedical research. To the scientists responsible for making the core facility operate as smoothly as possible, that makes a world of difference. “When you’re in the life sciences in addition to human biomedical [research], you’re out there in the world of things that haven’t been sequenced before, or haven’t been sequenced particularly well,” says Ken Dewar, a principal investigator at the Innovation Centre. To navigate this type of uncharted territory, scientists at the center…

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Tuesday, April 8, 2014

GC-Rich Genome of Pandoraea Bacterium Assembled with SMRT Sequencing

Scientists from the Institute of Biological Sciences at the University of Malaya recently published a description of Pandoraea sp. strain RB-44 in Genome Announcements, a journal from the American Society for Microbiology. The genome sequence was completed using Single Molecule, Real-Time (SMRT®) Sequencing. Pandoraea is a soil bacterium; this particular strain was collected from the site of a former landfill. Some strains of Pandoraea have been suggested as cystic fibrosis clinical pathogens, the authors report, though “their role in pathogenicity is still largely unknown.” Corresponding author Kok-Gan Chan and colleagues may have a new lead in that mystery. Their Pandoraea…

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Friday, March 21, 2014

ABRF Preview: Off to the Land of Core Labs and Hot Air Balloons

Members of the PacBio team will be heading down to Albuquerque this weekend for the annual conference of the Association of Biomolecular Resource Facilities (ABRF). It’s a big year for the association, which is celebrating its 25th anniversary, and we’re looking forward to participating. ABRF is a meeting where we connect with the most innovative leaders of the core facility community. As PacBio blog readers know, core labs are very important in the SMRT® Sequencing landscape. Last year we launched our directory of service providers that offer sequencing with the PacBio® platform, and many scientists have told us how useful…

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Friday, March 14, 2014

AGBT 2014 Presentation Videos: SMRT Sequencing at CSHL, Uppsala U., and Baylor College of Medicine

There were several excellent talks showcasing SMRT® Sequencing data at the annual Advances in Genome Biology and Technology conference. If you didn’t have the opportunity to see them in person, you can watch the recordings: From Cold Spring Harbor Laboratory, Dick McCombie described the need for de novo sequencing, which preserves structural information that can be missed with resequencing. Organisms presented include yeast, Arabidopsis, and rice. McCombie notes that in many cases, full chromosomes are assembled into single contigs with long-read sequencing. He also presented the longest read seen at AGBT: more than 54 Kb. Watch video: A near perfect…

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Monday, March 3, 2014

In Acinetobacter Study, Long Reads Aid in Defining Genomic Structure

A paper recently published in mBio, an open access journal from the American Society for Microbiology, reports on the sequencing and phylogenetic analysis of several drug-resistant strains of a pathogen found in hospitals. According to the authors, incorporating PacBio® sequence was critical for generating extremely long contigs for assembly and for accurately identifying chromosomal position and structure of genomic features associated with drug resistance. The publication, entitled “New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis,” from scientists at the J. Craig Venter Institute, as well as Case Western Reserve University and its…

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Tuesday, February 18, 2014

AGBT Day 3 Highlights: Single Contigs, Dazzling Assemblers, Novel Isoforms & Honey Algorithms

Friday morning’s talks were exceptional, and included genomics heavy-hitters Dick McCombie and Gene Myers — both scientists who were truly influential in sequencing the human genome so many years ago. They have kept pushing boundaries, and their talks were fascinating. Cold Spring Harbor Laboratory’s McCombie offered a presentation based on a late-breaking abstract showing the importance of de novo assembly — rather than resequencing, which can miss structural differences — using SMRT® Sequencing. He showed data from genome sequences of two strains of yeast (S. cerevisiae and S. pombe), both of which were generated using P5-C3 chemistry with BluePippin™ size…

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Saturday, February 15, 2014

AGBT Day 1 & 2 Highlights: Hello GRCh38 & SMRT Sequencing for Pathogen Screening

AGBT 2014 is off to a roaring start – the opening reception was hastily moved indoors when an impressive thunderstorm joined the party. Wednesday’s kickoff plenary session offered an insightful view of the recently released human genome reference, known as GRCh38, which is available with GenBank accession GCA_000001405.15. Valerie Schneider from the National Center for Biotechnology Information gave a presentation on the latest build, highlighting improvements that range from alternate loci to modeled centromeres to error correction of individual bases. The Genome Reference Consortium resolved more than 1,000 reported issues from build 37 with the release of this new build…

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Tuesday, February 11, 2014

AGBT 2014 Preview: Long reads, long flight, long days!

We are flying cross-country to Marco Island, Florida, to attend the fifteenth annual Advances in Genome Biology and Technology conference and, as we have done for years now, we are proud to be sponsoring the event. This year we look forward to connecting with the many researchers who already work with SMRT® Sequencing data, and to meeting others whose scientific efforts could benefit from our technology’s uniquely long reads and base modification information. Here are some of the presentations we’ll be attending: Evan Eichler, University of Washington, “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism” …

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Wednesday, January 29, 2014

At Plant & Animal Genome Workshop, Users Showcase Projects Enabled by SMRT Sequencing

Earlier this month, we hosted a workshop at the International Plant & Animal Genome (PAG) conference in San Diego entitled “A SMRT® Sequencing Approach to Reference Genomes, Annotation, and Haplotyping.” PacBio users presented data on various projects that have benefited from long-read sequence data, including several that had previously been attempted with short-read technologies without success. We were delighted to see reports on newer features of SMRT Sequencing, including full-length isoforms, automated haplotyping, and more. Here’s a recap, as well as links to video recordings of the presentations: Chongyuan Luo, a scientist from Joe Ecker’s lab at the Salk Institute…

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