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Thursday, April 30, 2020

Sequencing 101: Looking Beyond the Single Reference Genome to a Pangenome for Every Species

What is a Pangenome? A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. Unless you have an identical twin, no other person has a genome that is identical to yours. The same is true for other animal, plant, and microbial species that reproduce sexually: the genomes of individuals are unique. Less well known, but equally true, is that individual members of a species do not always share even the exact same genes. Nevertheless, scientists mostly use a single reference genome to represent an entire species: one human genome, one…

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Tuesday, April 28, 2020

Delivering New Insights into Cancer Research: SMRT Sequencing Case Studies

Will the next big cancer breakthrough be in immunotherapy? Therapeutic modification of the tumor microenvironment or microbiome? Or early detection and screening?  Whatever the result, long-read sequencing technology can play a pivotal part in the discovery process, according to Meredith Ashby, PacBio’s director of Market Strategy for Microbial Genomics, Cancer and Immunology. In a recent article for Lab Compare, Ashby highlighted some of the ways Single Molecule, Real-Time (SMRT) Sequencing has given researchers a deeper understanding of tumors at the genomic and transcriptomic level. The benefits of applying long-read sequencing to cancer research By spanning very large structural variants in…

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Wednesday, April 22, 2020

Sequencing 101: Why Are Long Reads Important for Studying Viral Genomes?

The COVID-19 pandemic has brought a sudden urgency to virus research and led many of us to dig more deeply into all the tools available for characterizing viral genomes, from RT-PCR to DNA sequencing. For all their outsized impact on human health, viruses have remarkably small and simple genomes, some just a few thousand bases in length, and most lacking any repetitive structures. With such tidy genomes, you may wonder, why would scientists want to sequence them with a long-read technology like PacBio HiFi reads? Quasispecies develop as variants are introduced to the viral genome through mutations. While it is…

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Wednesday, April 15, 2020

Go Big or Go Home — Tackling a Giant Genome

California redwoods: Not only are they giants in height and age (up to 379 feet high, 29 feet round, and thousands of years old), but the famous towering trees are also derived from a massive 27 Gb genome. Seeking a sequencing challenge for the Sequel II System, we picked the California redwood, or Sequoia sempervirens as it’s known to scientists. There also happened to be several fine specimens at nearby Stanford University. A small crew of PacBio scientists — Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), and Michelle Vierra (@the_mvierra) — headed to campus to acquire samples equipped with ice, scissors,…

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Monday, April 13, 2020

How Long-read Sequencing Can Help Researchers Address Pressing Questions in COVID-19 Pandemic

Herculean efforts are being made by scientists around the world to respond quickly to the COVID-19 crisis in a race to understand the virus causing the pandemic and develop diagnostics, vaccines, and therapeutics. But many research questions remain. How can long-read SMRT Sequencing technology help fill the gaps? PacBio microbiology expert Meredith Ashby highlighted several opportunities to support coronavirus research in a recent webinar as part of a day-long virtual conference hosted by LabRoots.    Sequencing the viral genome Understanding the basic biology of the virus is essential, and the more detailed our investigation, the better.  Highly accurate, long-read sequencing…

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Wednesday, April 8, 2020

In Battle Against COVID-19 Pandemic, Scientists Turn to PacBio Sequencing

Image by Miroslava Chrienova from Pixabay Our team is proud to announce that PacBio has been working closely with customers to help in the fight against the COVID-19 pandemic. Scientists in commercial, academic, and government research teams are using highly accurate SMRT Sequencing data to resolve variants of the SARS-CoV-2 virus that exist within one individual or across a population of patients, which is critical to developing and maintaining effective diagnostics, vaccines, and therapeutics. Many of these efforts are powered by our HiFi reads, which are both long and highly accurate. Such reads are well-suited for applications like viral sequencing,…

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Tuesday, April 7, 2020

Sequencing 101: Video Introduction to PacBio Sequencing and the Sequel II System

We’re pleased to release a short video describing PacBio Sequencing and our latest platform, the Sequel II System. If you’ve ever wondered how Single Molecule, Real-Time (SMRT) Sequencing works, what the Sequel II System is, and what applications are available, this video is a great place to start. We are excited to share the capabilities of our Sequel II System as it makes SMRT Sequencing affordable for scientists in any lab and provides comprehensive views of genomes, transcriptomes, or epigenomes. The Sequel II System also produces highly accurate long reads, known as HiFi reads, to deliver the highest quality sequencing…

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Wednesday, April 1, 2020

HiCanu for HiFi Reads Produces First Assembly of Human Segmental Duplications and Centromeres

UPDATE — September 1, 2020: This paper is now published in Genome Research. ORIGINAL POST — April 1, 2020 In a new preprint, scientists from the National Human Genome Research Institute, the University of Washington, and other institutions describe HiCanu, a modified version of the Canu assembler designed specifically for PacBio HiFi reads. The team put the new assembler through its paces, reporting that it significantly outperformed traditional assembly methods — even getting through centromeres, segmental duplications, and other notoriously difficult regions. As lead authors Sergey Nurk (@sergeynurk) and Brian P. Walenz, corresponding authors Sergey Koren (@sergekoren) and Adam Phillippy…

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PacBio Grants Equity Incentive Award to New Employee

Friday, December 3, 2021

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