PacBio - Monthly Newsletter (May)

pacbio_shortlogo_color_rgb-01.jpgSo much is happening in the world of PacBio it is hard to keep up! The Sequel II has hit the ground running and it is exciting to see what researchers are doing with this technology now that PacBio reads are highly accurate, low cost and high throughput.

PacBio Sequel II Service Launched in Australia


Finally, we now have PacBio Sequel II service launched in Australia through an AGRF/UQ collaboration, and they are CSP, meaning you can be assured of your project being conducted to PacBio standards.

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SMRT Leiden Online - Changing the World One Molecule at a Time!

The Global SMRT Community Conference on Soon in May!

SMRT Leiden is an annual conference co-hosted with the Human Genetics Center of the Leiden University Medical Center in the Netherlands, where speakers and attendees engage on topics across our full range of applications from research areas including plant and animal research, human biomedical research, microbial genomics, and SMRT Informatics.  

For a recap of the content of the past four years of SMRT Leiden, click here

SMRT Leiden 2020 brings together the Global SMRT Community for engaging science and idea exchange, with more than 20 key experts and opinion leaders  sharing scientific discoveries and novel analytical achievements enabled by PacBio sequencing platforms.

All presentations will be available on-demand in early May, followed by live Q&A sessions held later in the month. SMRT Leiden speakers will address your questions on the topics of plant and animal research, human biomedical research, microbial genomics, and SMRT Informatics covering all application areas, including whole genome sequencing and annotation, targeted sequencing, metagenomics, and epigenetics

Keynote Speakers:

  • Erich Jarvis, Ph.D., Rockefeller University, USA
  • Ana Conesa, Ph.D., University of Florida, USA
  • Hagen Tilgner, Ph.D., Weill Medical College of Cornell University, USA
  • Jennifer Ong, Ph.D., New England Biolabs, USA
  • Sergey Koren, Ph.D., National Institutes of Health, USA
  • Kevin Fengler, Ph.D., Corteva Agriscience, USA

Presentations will be available on-demand on the 12th of May 2020, followed by live Q&A sessions on the 26th - 29th of May 2020, 14:00 - 15:30 GMT

Register now to get access! SMRT Leiden is FREE and open to all members of the scientific community.

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PacBio Webinar Series - Upcoming Webinars

Bioinformatics Solutions for pacBio HiFi Reads

The release of the PacBio Sequel II System in 2019 brought dramatic throughput improvements and protocols for producing a new data type, highly accurate long reads or HiFi reads.

PacBio is the only sequencing technology to offer highly accurate long reads (HiFi reads) that provide Sanger-quality accuracy (>99%) with the read lengths needed for assembly of complex genomes. The long length and high accuracy of HiFi reads makes them the ideal starting point for many applications, and one area of major interest is genome assembly. HiFi assembly is faster, cheaper, more accurate, and easier to phase than standard long-read assembly.

By attending this webinar you will learn:

  1. The difference between long reads and HiFi reads
  2. The strengths of HiFi read assembly for human, plant, animal, and insect genomes
  3. About the step-by-step instructions on how to assemble HiFi reads using the publicly available FALCON package, which can be found here

Date: Thursday 14th May, 2020
Time: 1:00pm Melbourne
Speaker: Khi Pin Chua, Ph.D. Field Applications Support, Bioinformatics, PacBio, Asia Pacific

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Increasing Solve Rates for Rare and Mendelian Diseases with Long-Read Sequencing

The current solve rate for rare diseases is <50% for whole exome and genome sequencing using massively parallel short reads. What if you could now map the causative variant for cases that were previously unsolved? Register for our webinar on how long-read sequencing is being incorporated for rare Mendelian diseases and learn about:

  • Why highly accurate HiFi reads matter in long-read sequencing.
  • What can be detected with HiFi reads that is missed with standard sequencing methods.
  • How long-read sequencing can help increase the solve rates in rare Mendelian disease.
  • How Dr. Kristen Sund from Cincinnati Children's Hospital Medical Center has used long-read sequencing to solve rare neurological diseases involving complex structural rearrangements that were previously unsolved with standard methods.

Date: Wednesday 27th May, 2020
Time: 3:00am Melbourne
Speakers: Aaron Wenger, Ph.D. Principle Scientist, PacBio & Kristen Sund, Ph.D. Clinical Fellow, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, PacBio

This webinar is early morning for Australia and New Zealand, but register now for the recording!

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COVID-19 Resources

egetimage-8.pngAs scientists worldwide seek to understand the COVID-19 pandemic, PacBio is proud to be able to provide tools for sequencing the SARS-CoV-2 virus and the related immune response. Explore the resources below and attend our webinar to learn how the critical efforts of genetic mutation profiling in viral RNA isolates, full-length B cell receptor profiling, and HLA and IGH haplotyping can be enabled with PacBio sequencing

aerf.pngDiscover Tools and Resources

Learn how to use HiFi reads to sequence SARS-CoV-2 and the related immune response

Discover more

aerf-a.jpegRegister for a Webinar

May 7th: Understanding the host immune response to SARS-CoV-2.

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arfea.pngTry a New Method

Use a long-amplicon protocol for SARS-CoV-2 sequencing.

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aerfare.jpegWatch a Recording

How to use long-read sequencing for COVID-19 research.

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Application Spotlight - Plant and Animal De Novo Genome Assembly

Tackling a genome project can offer unique challenges. Luckily, HiFi sequencing is making De novo assembly easier and more efficient by helping you:

  • Distinguish between very similar repeats
  • Tease apart different haplotypes
  • Speed up analysis when you are compute constrained

See how the assembly tools and genome projects below take advantage of these three benefits of HiFi sequencing data.

aerf.pngExplore a New Method

HiFi Assembler Series: HiCanu , near optimal repeat solution

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aerf-a.jpegAccess Accuracy

Beyond contiguity - Measuring the quality of genome assemblies.

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arfea.pngDiscover a Genome

A genome fit for a giant - sequencing the California redwood.

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aerfare.jpegWatch on Demand

Bioinformatics webinar: Practicalities of HiFi assembly.

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

pangenome2x-768x440.pngWhat is a Pangenome? 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 maize genome, one Staphylococcus aureus genome.   The Coining of the "Pangenome"  Around 2005, geneticists started to...

Read the full blog here

Data Release: HiFi Sequencing Results for Plants, Animals and Microbes

It's been more than a year since we introduced HiFi sequencing to generate highly accurate long reads. In that time, we've seen many PacBio users make HiFi sequencing their go-to setting because it's simple, reliable, and cost-effective. For scientists who have yet to generate their own HiFi data, we thought it might be helpful to publish a few data sets for exploration and analysis

In a new preprint, we have released HiFi data sets for five samples: mouse, frog, maize, strawberry, and a mock metagenome community. We like to think there's a data set for everyone here, whatever your research area of interest! Working with any of these HiFi read collections should offer a great introduction to this sequencing mode and show you why we often hear how easy it is to analyze HiFi data compared to traditional long reads.

Read the Full Blog Post Here

2020-03-03_12-26-29.jpg 2020-03-03_12-27-15.jpg 2020-03-03_12-27-29.jpg

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