August 19, 2021 | General
PacBio Certified Service Providers
Explore a list of PacBio certified service providers.
Asset Tag: de novo assembly
August 19, 2021 | Agrigenomics
Infographic — Gold-standard reference genomes accelerate science
Explore how high-quality genomes contribute to critical scientific endeavors.
August 19, 2021 | Infectious disease research
Infographic — A brief history of microbiology
Our understanding of microbiology has evolved enormously over the last 150 years. Few institutions have witnessed our collective progress more closely than the National Collection of Type Cultures (NCTC). In fact, the collection itself is a record of the many milestones microbiologists have crossed, building on the discoveries of those who came before. To date, 60% of NCTC’s historic collection now has a closed, finished reference genome, thanks to PacBio Single Molecule, Real- Time (SMRT) Sequencing. We are excited to be their partner in crossing this latest milestone on their quest to improve human and animal health by understanding the microscopic world.
August 19, 2021
Infographic — A genome fit for a giant – sequencing the California redwood
Explore how highly accurate long-read sequencing enabled sequencing the large and highly complex California redwood genome.
August 19, 2021 | Cancer research
Case Study — Scientists deconstruct cancer complexity through genome and transcriptome analysis
At Cold Spring Harbor Laboratory, scientists used SMRT Sequencing to decode one of the most challenging cancer genomes ever encountered. Along the way, they built a portfolio of open-access analysis tools that will help researchers everywhere make structural variation discoveries with long-read sequencing data.
August 19, 2021
Case Study — Pioneering a pan-genome reference collection
At DuPont Pioneer, DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in commercial crops such as maize, soybean, sorghum, sunflower, alfalfa, canola, wheat, rice, and others. They cannot afford to wait the years it has historically taken for high-quality reference genomes to be produced. Nor can they rely on a single reference to represent the genetic diversity in its germplasm.
August 19, 2021 | Cancer research
Brochure — Sequence cancer variants with confidence
To bring personalized medicine to all patients, cancer researchers need more reliable and comprehensive views of somatic variants of all sizes that drive cancer biology.
August 19, 2021 | Microbial sequencing methods
Case Study — Sequencing an historic bacterial collection for the future
The UK’s National Collection of Type Cultures (NCTC) is a unique collection of more than 5,000 expertly preserved and authenticated bacterial cultures, many of historical significance. Founded in 1920, NCTC is the longest established collection of its type anywhere in the world, with a history of its own that has reflected — and contributed to — the evolution of microbiology for more than 100 years.
August 19, 2021 | Products, procedures + protocols
Application brochure — HiFi reads for highly accurate long-read sequencing
Discover the benefits of HiFi reads and learn how highly accurate long-read sequencing provides a single technology solution across a range of applications.
August 19, 2021 | Sequencing methods
Application brief — Whole genome sequencing for de novo assembly
PacBio HiFi reads provide both long read lengths (up to 25 kb) and high accuracy (>99.9%) to quickly and affordably generate contiguous, complete, and correct de novo genome assemblies of even the most complex genomes.
August 19, 2021 | Human genetics research
Publication at a Glance — The complete sequence of a human genome
This landmark study by members of the Telomere-to-Telomer Consortium is the first fully complete assembly to be produced 20 years after the initial drafts of the human genome.
June 15, 2021
Uncovering Neurological Disorders Through an Examination of VNTRs
Many neurological diseases result from expansion of unstable variable nucleotide tandem repeats (VNTRs) that influence gene transcription of neighboring genes. In this talk, Dr. Henne Holstege presents research that investigated…
June 1, 2021
Evaluating the potential of new sequencing technologies for genotyping and variation discovery in human data.
A first look at Pacific Biosciences RS data Pacific Biosciences technology provides a fundamentally new data type that provides the potential to overcome these limitations by providing significantly longer reads (now averaging >1kb), enabling more unique seeds for reference alignment. In addition, the lack of amplification in the library construction step avoids a common source of base composition bias. With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical resequencing projects by assessing the quality of the raw sequencing data, as well as its use for SNP discovery and genotyping using the Genome Analysis Toolkit (GATK).
June 1, 2021
Sequencing and de novo assembly of the 17q21.31 disease associated region using long reads generated by Pacific Biosciences SMRT Sequencing technology.
Assessment of genome-wide variation revealed regions of the genome with complex, structurally diverse haplotypes that are insufficiently represented in the human reference genome. The 17q21.31 region is one of the most dynamic and complex regions of the human genome. Different haplotypes exist, in direct and inverted orientation, showing evidence of positive selection and predisposing to microdeletion associated with mental retardation. Sequencing of different haplotypes is extremely important to characterize the spectrum of structural variation at this locus. However, de novo assembly with second-generation sequencing reads is still problematic. Using PacBio technology we have sequenced and de novo assembled a tiling path of eight BAC clones (~1.6 Mb region) across this medically relevant region from the library of a hydatidiform mole. Complete hydatidiform moles arise from the fertilization of an enucleated egg from a single sperm and therefore carry a haploid complement of the human genome, eliminating allelic variation that may confound mapping and assembly. The PacBio RS system enables single molecule real time sequencing, featuring long reads and fast turnaround times. With deep sequencing, PacBio reads were able to generate a very uniform sequencing coverage with close to 100% coverage of most of the target interval regions covered. Due to long read lengths, the PacBio RS data could be accurately assembled.
June 1, 2021
Comparative genomics of Shiga toxin-producing Escherichia coli O145:H28 strains associated with the 2007 Belgium and 2010 US outbreaks.
Shiga toxin-producing Escherichia coli (STEC) is an emerging pathogen. Recently there has been a global in the number of outbreaks caused by non-O157 STECs, typically involving six serogroups O26, O45, 0103, 0111, and 0145. STEC O145:H28 has been associated with severe human disease including hemolytic-uremic syndrome (HUS), and is demonstrated by the 2007 Belgian ice-cream-associated outbreak and 2010 US lettuce-associated outbreak, with over 10% of patients developing HUS in each. The goal of this work was to do comparative genomics of strains, clinical and environmental, to investigate genome diversity and virulence evolution of this important foodborne pathogen.