As the foundation for scientific discoveries in genetic diversity, sequencing data must be accurate and complete. With highly accurate long-read sequencing, or HiFi sequencing, there is no longer a compromise between read length and accuracy. HiFi sequencing enables some of the highest quality de novo genome assemblies available today as well as comprehensive variant detection in human samples. PacBio HiFi libraries constructed using our standard library workflows require at least 3 µg of DNA input per 1 Gb of genome length, or ~10 µg for a human sample. For some samples it is not possible to extract this amount of…
In this video, PacBio scientists present ongoing improvements to the Integrative Genomics Viewer (IGV) and demonstrate how multiple new features improve visualization support for PacBio long-read sequencing data. The video describes these recent updates which include; quick consensus accuracy mode to hide random single-molecule errors, direct phasing of haplotypes using long-read evidence, and visual annotation of insertions and deletions relative to the reference with enumeration of gap size for individual reads. These new features are available now in the development version of IGV, which can be found at http://software.broadinstitute.org/software/igv/download_snapshot. The Sequel sequencing data used in this demonstration is also publicly…
Targeted sequencing experiments commonly rely on either PCR or hybrid capture to enrich for targets of interest. When using short read sequencing platforms, these amplicons or fragments are frequently targeted to a few hundred base pairs to accommodate the read lengths of the platform. Given PacBio’s long readlength, it is straightforward to sequence amplicons or captured fragments that are multiple kilobases in length. These long sequences are useful for easily visualizing variants that include SNPs, CNVs and other structural variants, often without assembly. We will review methods for the sequencing of long amplicons and provide examples using amplicons that range…
Jonas Korlach kicks off Day 2 of the 2018 User Group Meeting by discussing a recent collaboration and technique for low-input starting material and high quality de novo assembly projects. While new and not yet fully supported, many researchers have interest in starting with lower amounts of DNA for whole genome sequencing. This protocol requires Express Kit v2, which will be available in early 2019.
In this presentation, Justin Blethrow provides an overview of recent and upcoming developments across PacBio’s SMRT Sequencing product portfolio, and their implications for PacBio’s major applications. In presenting the product roadmap, he illustrates how key new products coming in 2019 will make SMRT Sequencing dramatically more affordable and easy to use, and how they will enable customers to routinely produce highly accurate, single-molecule long reads.
In this presentation, Andrew Clark from Cornell University describes work from a collaboration with Manyuan Long of the University of Chicago and Rod Wing of the University of Arizona to look at heterochromatic regions with long simple satellite repeats in drosophila genomes. The group used PacBio sequencing to create new genome assemblies of 10 drosophila species, including de novo assemblies of two individual flies using as little as 26 ng of gDNA.
To start Day 2 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on lowering DNA input amounts for SMRT Sequencing workflows. Updates include a more robust shearing method, a revised AMPure size selection, and introduction of multiplexing low input samples. Finally, the use of HiFi sequencing with low input results in a more complete genome assembly. Jonas closes by mentioning that the low DNA input protocol is now available and further advancements to lower input requirements even more will open opportunities for different samples, such as cancer needle biopsies.
To start Day 1 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on the latest releases and performance metrics for the Sequel II System. The longest reads generated on this system with the SMRT Cell 8M now go beyond 175,000 bases, while maintaining extremely high accuracy. HiFi mode, for example, uses circular consensus sequencing to achieve accuracy of Q40 or even Q50.
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.
In this PacBio User Group Meeting presentation, Eugenio Daviso from Covaris talks about the use of adaptive focused acoustics for gentle cell lysis and extraction of high molecular weight DNA.
In this PacBio User Group Meeting presentation, Erin Bernberg from the University of Delaware reports on using the Agilent Femto Pulse System for high-resolution, highly sensitive fragment analysis and on the low DNA input protocol, which her team used for a recent study of ice worms.
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.…
In this webinar you will hear how several researchers have overcome the challenges of sequencing organisms with small body size using the new low and ultra-low DNA input methods from PacBio. Learn about the advantages of using highly accurate long reads (HiFi reads) to sequence and de novo assemble genomes of single individuals.
A high-quality reference genome is an essential tool for studies of plant and animal genomics. PacBio Single Molecule, Real-Time (SMRT) Sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. PacBio is the core technology for many large genome initiatives, however, relatively high DNA input requirements (5 µg for standard library protocol) have placed PacBio out of reach for many projects on small, non-inbred organisms that may have lower DNA content. Here we present high-quality de novo genome assemblies from single invertebrate individuals for two different species: the Anopheles…