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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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Tuesday, June 2, 2015

In Assembler Evaluation, Scientists Recommend Non-hybrid Approach to Bacterial Genomes

A new publication in Nature Scientific Reports recommends using only the PacBio® system to sequence bacterial genomes for the best chance of generating an accurate and finished assembly. The paper, “Completing bacterial genome assemblies: strategy and performance comparisons,” reviews several different long-read assembly methods for bacterial genomes. Authors Yu-Chieh Liao, Shu-Hung Lin, and Hsin-Hung Lin from the Institute of Population Health Sciences in Taiwan note that while several methods exist, efforts to evaluate and compare them have been insufficient. They set out to thoroughly assess these methods, which include hybrid assembly protocols as well as long-read-only protocols. Long-read technology appealed…

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Friday, January 23, 2015

Breaking New Frontiers in Grass Genomics to Understand Drought Tolerance with the 2014 SMRT Grant Program Winner: Oropetium thomaeum

Emerging from a myriad of interesting genome nominations, from the American cranberry to South American prawns and African Guava, Oropetium thomaeum submitted by Todd Mockler at the Donald Danforth Plant Science Center was selected as the first winner of the “Most Interesting Genome in the World” SMRT® grant program in 2014.  Also affectionately known as Oro, this grass species can be  revived with water after a long drought exposure. At 250 Mb, the genome is also the smallest amongst grasses due to compaction of complex repeat and gene structures, including previously identified expansions in osmoprotectant biosynthesis pathways. Kicking off the…

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Monday, September 22, 2014

Maryland Scientists Produce High-Quality, Cost-Effective Genome Assembly of Loa loa Roundworm Using SMRT Sequencing

A paper just released in BMC Genomics details what authors call “the most complete filarial nematode assembly published thus far at a fraction of the cost of previous efforts.” The project was performed using the PacBio® RS II DNA Sequencing System by scientists at the University of Maryland School of Medicine’s Institute for Genome Sciences and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases. In this genome sequencing effort, scientists generated a de novo assembly of Loa loa, a roundworm that infects humans. L. loa, transmitted to humans by deer flies, causes loiasis. The…

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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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Wednesday, February 12, 2014

Data Release: ~54x Long-Read Coverage for PacBio-only De Novo Human Genome Assembly

We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x.  This long-read data has enabled the generation of the first de novo human genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset. The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which…

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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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Tuesday, January 21, 2014

Genome Research Paper: Resolve Complex Genomic Regions for a ‘Fraction of the Cost’ With SMRT Sequencing

A new Genome Research paper describes the application of Single Molecule, Real-Time (SMRT®) Sequencing to resolve repeat-heavy genomic regions in important reference genomes such as human and chimpanzee. In the process, the authors drew some important conclusions about cost, pooling, and coverage requirements for this type of work. “Reconstructing complex regions of genomes using long-read sequencing technology” comes from lead author John Huddleston and senior author Evan Eichler at the University of Washington, along with collaborators at Washington University, the University of Bari, Bilkent University, and Pacific Biosciences. In the paper, Eichler and his collaborators note the steep cost of…

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Monday, January 13, 2014

Data Release: Preliminary de novo Haploid and Diploid Assemblies of Drosophila melanogaster

Model organisms such as yeast, Arabidopsis and Drosophila have been essential to progress in genetic and biomedical research for more than 100 years.  Model organisms are the best, fastest, most effective way to advance science especially when human experimentation may not be feasible. Numerous biological principles have been elucidated using model organisms, including Nobel-prize winning discoveries by Thomas Hunt Morgan that genes are carried on chromosomes; by Hermann Muller for the discovery that X-ray irradiation causes mutations; and by Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus for their discoveries revealing the genetic control of early embryonic development - all…

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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, July 29, 2013

As Cores Upgrade to PacBio RS II, Users Report Data and Progress

As PacBio customers are upgrading to the new PacBio® RS II System, some of our core lab users have already begun blogging about the improved results. At the University of Maryland’s Institute for Genome Sciences (IGS), for example, one blogger posted data comparing read length, read count, and throughput for the PacBio RS and PacBio RS II. The post reports a comparison of an 8 Kb Mycobacterium project run on the PacBio RS and again on the PacBio RS II, finding that with the upgrade, “we see an almost 3x increase in total yield [per SMRT Cell], while read lengths…

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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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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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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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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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