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Friday, February 5, 2021

Webinar: Bioinformatics lunch & learn – HiFi assembly

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.…

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Friday, February 5, 2021

PacBio Workshop: Understanding the biology of genomes with HiFi sequencing

The utility of new highly accurate long reads, or HiFi reads, was first demonstrated for calling all variant types in human genomes. It has since been shown that HiFi reads can be used to generate contiguous, complete, and accurate human genomes, even in repeat structures such as centromeres and telomeres. In this virtual workshop scientists from PacBio as well as Tina Graves-Lindsay from the McDonnell Genome Institute at Washington University share the many improvements we’ve made to HiFi sequencing in the past year, tools that take advantage of HiFi data for variant detection and assembly, and examples in numerous genomics…

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Friday, February 5, 2021

PAG Conference: PacBio update on products and HiFi applications

In this talk at PAG 2020, PacBio Plant and Animal Sciences Marketing Manager Michelle Vierra discusses recent updates to Single Molecule, Real-Time (SMRT) Sequencing technology, including the Sequel II System, updated protocols for low-input as well as other upcoming developments.

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Friday, February 5, 2021

Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research

In this Labroots webinar, Meredith Ashby, Director of Microbial Genomics at PacBio, describes the utility of highly accurate long-read sequencing, known as HiFi sequencing, to understand the SARs-CoV-2 viral genome. HiFi sequencing enables mutation phasing and rare variant detection to understand viral stability and mutation rates, as well as providing insights into viral population structure for monitoring viral evolution. Ashby also shares how HiFi sequencing can be used to explore the host immune response to COVID-19, specifically by providing full-length sequencing of the B cell repertoire, IGH locus and HLA genes. Access additional COVID-19 Sequencing Tools and Resources at at…

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Friday, February 5, 2021

AGBT Presentation: Studying CRISPR guide RNA specificity by amplification-free long-read sequencing

At AGBT 2020, Adam Ameur from Uppsala University discussed the use of long-read PacBio sequencing to detect off-target results from CRISPR/Cas9 gene editing studies. His team uses HiFi reads from the Sequel II System to perform whole genome sequencing and figure out exactly where guide RNAs bind. In one example using a human embryonic kidney cell line, they found 55 off-target sites for three guide RNAs. Ameur’s group has already generated preliminary data on results from editing living cells.

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Friday, February 5, 2021

AGBT Presentation: Generating high quality human reference assemblies with PacBio sequencing

Tina Graves-Lindsay from the McDonnell Genome Institute reports at AGBT 2020 on how her team is using PacBio sequencing to produce reference-grade human genome assemblies. With highly accurate HiFi reads, no error correction step is needed during the sequencing and analysis process, and they can produce reference-grade assemblies with half the sequence coverage needed before. They are now generating diploid assemblies and will be contributing to the human pangenome reference project.

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Friday, February 5, 2021

Webinar: Long HiFi reads for high-quality genome assemblies

In this LabRoots webinar, Jonas Korlach the CSO of PacBio provides an introduction to PacBio HiFi sequence reads, which are both long (up to 25 kb currently) and accurate (>99%) at the individual single-molecule sequence read level andhave allowed for advances in de novo genome assemblies. Korlach reviews the characteristics of HiFi read data obtained with the Sequel II System, followed by examples of high-quality genome assemblies for human, plant and animal genomes including the different aspects of evaluating genome assemblies (contiguity, accuracy, completeness and allelic phasing) and illustrates their high quality by examples of resolving centromeres, telomeres, segmental duplications…

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Friday, February 5, 2021

ASHG CoLab: PacBio HiFi reads for comprehensive characterization of genomes and single-cell isoform expression

In this ASHG 2020 CoLab presentation hear Principal Scientists, Aaron Wenger and Elizabeth Tseng share how highly accurate long reads (HiFi reads) provide comprehensive variant detection for both genomes and transcriptomes. Aaron Wenger describes how new improvements in protocols and analysis methods have increased scalability and accuracy of variant calling. As demonstrated in the precisionFDA Truth Challenge V2, HiFi reads (>99% accurate, 15 kb – 20 kb) now outperform short reads for single nucleotide and structural variant calling and match for small indels. This includes calling >30,000 small variants and >10,000 structural variants missed by short reads, many in medically…

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Friday, February 5, 2021

Educational Video: Variant Detection with HiFi Reads – Understanding Results from the precisionFDA Truth Challenge

In this short video, Aaron Wenger, a Principal Scientist at PacBio, explains what highly accurate long reads, or HiFi reads, are and how they help to detect all variant types including single nucleotide, indels, and structural variants. He goes on to recap the precisionFDA Truth Challenge V2 which used Genome in a Bottle (GIAB) benchmarks to evaluate various sequencing technologies. In the 2020 challenge, when ranked for accuracy, PacBio HiFi reads delivered the highest precision and recall in all categories.

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Friday, February 5, 2021

Webinar: Increasing solve rates for rare and Mendelian diseases with long-read sequencing

Dr. Wenger gives attendees an update on PacBio’s long-read sequencing and variant detection capabilities on the Sequel II System and shares recommendations on how to design your own study using HiFi reads. Then, Dr. Sund from Cincinnati Children’s Hospital Medical Center describes how she has used long-read sequencing to solve rare neurological diseases involving complex structural rearrangements that were previously unsolved with standard methods.

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Friday, February 5, 2021

Webinar: SMRT Sequencing applications for human genomics and medicine

In this webinar, Adam Ameur of SciLifeLab at Uppsala University shares how he uses Single Molecule, Real-Time (SMRT) Sequencing applications for medical diagnostics and human genetics research, including sequencing of single genes and de novo assembly of human genomes as well as a new method for detection of CRISPR-Cas9 off-targets.

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Friday, February 5, 2021

Video Poster: High-throughput HiFi library workflow for human whole genome sequencing on the Sequel II System

Recent advances in sequencing chemistry and software in the Sequel II System enable generating highly accurate long reads that are up to 25 kb in length with >99% accuracy. The high quality HiFi reads are suitable for variant detection of all types, from single nucleotides to structural variants. PacBio offers an end-to-end solution from sample preparation to data analysis. However, library construction is still a bottleneck making it difficult to implement into a high-throughput workflow for sequencing large number of samples. Input DNA requirements, DNA shearing and size-selection/fractionation are the most critical and challenging steps in the current procedure. In…

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Friday, February 5, 2021

ASHG PacBio Workshop: Latest product and application updates

In this ASHG 2020 PacBio Workshop Jonas Korlach, CSO, shares how the new PacBio Sequel IIe System makes highly accurate long-read sequencing easy and affordable so?all scientists can gain comprehensive views of human genomes and transcriptomes. He goes on to provide updates on the applications including human WGS for variant detection, de novo genome assembly, single-cell full-length RNA sequencing, and targeted sequencing using PCR and No-Amp methods.

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