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Thursday, September 17, 2015

SMRT Data Analysis: Updates from our Developers Conference

Last month we hosted a SMRT® Informatics Developers Conference, bringing together 150 developers with a passion for improving tools and resources. Our team came back brimming with enthusiasm for tools that will be released in the coming months, and humbled by the commitment we saw from the bioinformatics community to help scientists make SMRT Sequencing data increasingly useful. Thanks to the National Institute of Standards and Technology for hosting our meeting on their campus right before the Genome in a Bottle workshop.The big news we shared with attendees is that the PacBio® System will now output industry-standard BAM files instead…

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Tuesday, September 8, 2015

Webinar: Long Fragment Capture for SMRT Sequencing

Roche recently posted this recording of a webinar walking through long fragment capture with SMRT® Sequencing. “Long Genomic DNA Fragment Capture and SMRT Sequencing Enables Accurate Phasing of Cancer and HLA Loci” is a great backgrounder for scientists interested in using the Roche NimbleGen SeqCap EZ System for target enrichment prior to sequencing on the PacBio® system.The webinar features Denise Raterman from Roche NimbleGen and our own bioinformatics expert Lawrence Hon. Raterman provides a detailed review of the SeqCap EZ workflow, pointing out the specific steps that differ for SMRT Sequencing. The method can be used to capture up to…

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Thursday, August 20, 2015

The Gapless Assembly: Scientists Describe Workflow for Producing Complete Eukaryote Genome

Sunflowers with verticillium wilt caused by V. dahliaeIn a new mBio publication, scientists from Wageningen University and KeyGene in The Netherlands report results from several strategies used to assemble the genome of a filamentous fungus, and describe the specific pipeline they recommend for sequencing and assembling eukaryotic genomes.“Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome” comes from lead authors Luigi Faino and Michael Seidl, senior author Bart Thomma, and collaborators. Using Verticillium dahliae as a model, which is a plant pathogen responsible for the damaging verticillium wilt disease in many crop species, they compared short-read and…

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Wednesday, August 12, 2015

Using SMRT Sequencing, Scientists Uncover Unexpected Transcript Diversity in Fungi

A new PLoS One publication from scientists at the Joint Genome Institute, University of Minnesota, and other organizations demonstrates that fungal genomes may contain far more transcript diversity than previously thought. In “Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing,” lead author Sean Gordon, senior author Zhong Wang, and collaborators used long-read isoform sequencing to characterize four fungal species. In addition to widespread alternative splicing, they found evidence of polycistronic transcription units that could be important engineering targets for genetic manipulation of fungi. The scientists turned to SMRT® Sequencing to escape the limitations of short-read transcriptome sequencing. “The…

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Wednesday, December 4, 2013

In RNA-seq Study, Long PacBio Reads Allow for Detection of Full-Length and Novel Isoforms

A new paper out in PNAS details the usefulness of long reads for isoform sequencing. “Characterization of the human ESC transcriptome by hybrid sequencing” comes from lead author Kin Fai Au and senior author Wing Wong at Stanford University as well as a number of collaborators. The authors detail the problem that they see with current RNA-seq studies: the inability to capture full-length mRNA isoforms (averaging about 2,500 bases) by using reads of just a few hundred base pairs. “We are still far from achieving the original goals of RNA-Seq analysis, namely the de novo discovery of genes, the assembly…

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Tuesday, December 3, 2013

PacBio Partners with Sanger Institute and Public Health England to Finish 3,000 Bacterial Genomes

Sanger's Genome Campus We are pleased to announce a new collaboration with the Wellcome Trust Sanger Institute and Public Health England to complete the sequences of 3,000 bacterial genome strains from PHE’s National Collection of Type Cultures (NCTC). Sequencing will be performed on the PacBio® RS II DNA Sequencing System at the Sanger Institute. The three-year project could double the number of finished microbial genomes in GenBank. The NCTC is one of the world’s premier collections for bacterial strains, but most bacteria in NCTC currently have no genome references. Combining reference genomes with the wealth of historical and biological information…

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Wednesday, November 20, 2013

New Publication Demonstrates Long-Read Sequences Needed to Thoroughly Resolve Short Tandem Repeats

In a new paper reporting a protocol for using short-read sequence data to locate short tandem repeats (STRs), scientists find that long-read sequence information is necessary to resolve regions with repeat complexity, extreme GC content, and other challenging factors. Their solution is to use short-read data to find STRs, and then to use long-read sequencing to fully characterize those repeat expansions. The Bioinformatics publication is entitled “Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing” and came from scientists Koichiro Doi, Shinichi Morishita, et al. at the University of Tokyo. They focused on resolving STRs across…

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Thursday, November 14, 2013

ASHG Workshop Recordings: Resolving Structural Variation in Human Genomes

We hosted a structural varation workshop at the annual meeting of the American Society of Human Genetics, and were pleased to see that the speakers' presentations really resonated with attendees – the event was standing-room-only! Jonas Korlach, PacBio CSO, opened the session by sharing a brief update on SMRT® technology, noting that the new P5-C3 chemistry delivers 50% of bases in 10 kb or longer reads. View presentation recording Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discussed his use of the PacBio® system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a…

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Thursday, November 7, 2013

Event Recap: Fall User Group Meeting Presentations & Review

In September we were excited to have 100+ customers gather in Palo Alto, Calif., to discuss their use of Single Molecule, Real-Time (SMRT®) Sequencing and hear about what’s next for the PacBio® RS II. Many thanks to all the scientists who attended and shared their experiences. For anyone who couldn’t make it, we’ve included some highlights from each talk below (and links to full presentations when possible): Chongyuan Luo from the Ecker lab at the Salk Institute for Biological Studies spoke about studying the genome and epigenome of several Arabidopsis thaliana strains using SMRT Sequencing. Luo noted that Arabidopsis is…

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Wednesday, November 6, 2013

At Institute for Genome Sciences, Long Reads Offer New Path to Finished Genomes

The Genomics Resource Center (GRC) at the Institute for Genome Sciences (IGS) has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’ Both GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute for Genomic Research (TIGR), led by Claire Fraser, joined the University of Maryland School of Medicine. “The group of faculty and senior staff that came here to start the institute was heavily focused on infectious disease…

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Monday, November 4, 2013

Comparative Transcriptome Analysis: Insights from a Single SMRT Cell

In a new paper published in the journal Gene, scientists from Rutgers University and King’s College London report the use of a single SMRT® Cell to sequence and assemble more than 400 wheat-storage protein transcripts from 10 strains of the crop. In “PacBio sequencing of gene families — A case study with wheat gluten genes,” authors Wei Zhang, Paul Ciclitira, and Joachim Messing note that traditional studies of these cDNA sequences are so costly and labor-intensive that they have not allowed for intensive study of “the variation of each orthologous gene copy among cultivars.” That kind of study for complex…

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Tuesday, October 22, 2013

Data Release: Long-Read Shotgun Sequencing of a Human Genome

In order to help evaluate the utility of long, unbiased sequence reads for characterizing structural variation in the human genome using our recently released P5-C3 scaffolding sequencing chemistry, we have collected 10x long-read, shotgun coverage of a human genome sample. The human genome harbors many structural variations, including variable number tandem repeats, deletions, insertions, inversions, and repetitive mobile elements, which are often difficult to resolve using short-read technologies. We hope this data set will be of value to the bioinformatic and scientific community studying various forms of structural variation across the human genome. To access the full data set, simply…

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Thursday, October 17, 2013

Stanford Team Finds Novel Transcripts Using Long-Read Isoform Sequencing

An advance online publication in Nature Biotechnology from Michael Snyder’s lab at Stanford University demonstrates the utility of long-read sequencing for assessing transcribed regions across the human genome. Long PacBio reads were able to completely cover full-length RNA molecules, characterizing genetic regions that have not been previously annotated. The paper, entitled “A single-molecule long-read survey of the human transcriptome,” reports the application of Single Molecule, Real-Time (SMRT®) Sequencing to studying RNA, comparing it to results from libraries sequenced with a 454® instrument. The scientists sequenced cDNA synthesized from pooled RNA gathered from 20 human organs and tissues in order to…

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Monday, October 7, 2013

Characterizing Structural Variation in the Human Genome: ASHG 2013 Workshop and Presentations

We are excited to participate in the annual American Society of Human Genetics meeting again this year on October 22-26 in Boston, MA. With so many new PacBio® technology advances since last year, we wanted to give you a preview of how users are applying SMRT® Sequencing to better elucidate a variety of complex regions in the human genome. On Thursday, October 24, we’ll be hosting a luncheon workshop from 12:30 p.m. to 2:00 p.m. entitled ‘Characterizing Structural Variation in the Human Genome Using Long-Read SMRT Sequencing.’ Join us in room 152 of the convention center (BCEC) to hear from…

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Thursday, October 3, 2013

New Chemistry for PacBio RS II Provides Average 8.5 kb Read Lengths for Complex Genome Studies

Our R&D team has been focusing on chemistry improvements for the PacBio® RS II sequencer and today we are pleased to announce our newest reagent combination, the P5 DNA polymerase with C3 chemistry (P5-C3). Together, they extend our industry-leading sequencing read lengths to an average of approximately 8.5 kb, with the longest reads exceeding 30,000 bases. The new chemistry includes photo-protected dyes to shield the P5 polymerase from laser-induced damage. With this new protection, the sequencing polymerase is able to generate much longer reads from a single DNA-template molecule.  Our previously released chemistry, P4-C2, has been successfully used by many…

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