In this presentation, Elizabeth Tseng explains how PacBio’s full-length RNA Sequencing using the Iso-Seq method can characterize full-length transcripts without the need for computational transcript assembly. The Iso-Seq method is fully supported bioinformatically through PacBio’s SMRT Analysis software that outputs high-quality, full-length transcript sequences that can be used for genome annotation and novel gene discovery. Elizabeth shows that the highly accurate reads can be used to discover allelic-specific isoform expressions in transcriptome data.
In this PacBio User Group Meeting presentation, PacBio scientist Meredith Ashby shared several examples of analysis — from full-length 16S sequencing to shotgun sequencing — showing how SMRT Sequencing enables accurate representation for metagenomics and microbiome characterization, in some cases even without fully assembling genomes. New updates will provide users with a dedicated microbial assembly pipeline, optimized for all classes of bacteria, as well as increased multiplexing on the Sequel II System, now with 48 validated barcoded adapters. That throughput could reduce the cost of microbial analysis substantially.
Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…
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…
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 webinar, Kristin Mars, Sequencing Specialist, PacBio, presents an introduction to PacBio’s technology and its applications followed by a panel discussion among sequencing experts. The panel discussion addresses such things as what long reads are and how are they useful, what differentiates PacBio long-read sequencing from other technologies, and the applications PacBio offers and how they can benefit scientific research.
Structural variants (SVs, differences >50 base pairs) account for most of the base pairs that differ between two human genomes, and are known to cause over 1,000 genetic disorders including ALS, schizophrenia, and hereditary cancer. Yet, SVs remain overlooked in human genetic research studies due to the limited power of short-read sequencing methods (exome and whole genome sequencing) to resolve large variants, which often involve repetitive DNA. Recent advances in long-read sequencing have made it possible to detect the over 20,000 SVs that are now known to exist in a human genome. Corresponding advances in long-read SV calling algorithms have…
The bacteria living on and within us can impact health, disease, and even our behavior, but there is still much to learn about the breadth of their effects. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and the public alike. Scientists at Second Genome are hoping to apply these insights to improve human health, leveraging their bioinformatics expertise to mine bacterial communities for potential therapeutics. Recently they teamed up with scientists at PacBio to explore how long-read sequencing might supplement their short-read-based pipeline for gene discovery, using an environmental sample as a test…
With the Sequel II System powered by Single Molecule, Real-Time (SMRT) Sequencing technology and SMRT Link v8.0, you can affordably and effectively detect structural variants (SVs), copy number variants, and large indels ranging in size from tens to thousands of base pairs. PacBio long-read whole genome sequencing comprehensively resolves variants in an individual with high precision and recall. For population genetics and pedigree studies, joint calling powers rapid discovery of common variants within a sample cohort.
Discover the benefits of HiFi reads and learn how highly accurate long-read sequencing provides a single technology solution across a range of applications.
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.
Explore how long-read sequencing enables solving of rare and mendelian diseases.
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs. However, as next-generation sequencing technologies have developed, so too has RNA-seq. Now, RNA-seq methods are available for studying many different aspects of RNA biology, including single-cell gene expression, translation (the translatome) and RNA structure (the structurome). Exciting new applications are being explored, such as spatial transcriptomics (spatialomics). Together with new long-read and direct RNA-seq technologies and better computational tools for data analysis, innovations in RNA-seq are contributing to a fuller understanding of RNA biology, from questions…
Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis,…