In this PacBio Virtual Global Summit 2020 presentation, Mara Lawniczak of the Sanger Institute shares how generating reference genome has a transformative and immeasurable impact on the study of a species. A prime example of this is the journey of the past 18 years since the first Anopheles reference genome was sequenced. Anopheles mosquitoes are of particular interest to both medical research and evolutionary biologists because of their role in transmitting all human malaria and because of their notoriously porous species boundaries. Lawniczak described various projects ranging from population genomics on hundreds of wild caught specimens from across Africa including…
In this PacBio Virtual Global Summit 2020 presentation, Nicole Newell of PacBio provides an overview of the library preparation kits available for highly accurate long read (HiFi sequencing) applications. Learn more about PacBio at https://pacb.com/ Legal & Trademarks: Visit https://www.pacb.com/legal-and-trademarks/
Single Molecule, Real-Time (SMRT) Sequencing on the Sequel II System enables easy and affordable generation of high-quality de novo assemblies. With megabase size contig N50s, accuracies >99.99%, and phased haplotypes, you can do more biology – capturing undetected SNVs, fully intact genes, and regulatory elements embedded in complex regions.
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…
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, 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.
In this webinar we present the low DNA input workflow, from DNA requirements through library preparation and sequencing, for generation of high-quality genome assemblies of small-bodied organisms. In addition, we highlight the use of this workflow on the North American ice worm (Mesenchytraeus solifugus), which has a genome size of ~1.6 Gb and lives its entire life cycle in glacier ice, creating a unique opportunity to look at adaptation to harsh environments.
Mark Blaxter, project lead of the Sanger Institute’s Darwin Tree of Life, shared an update of the ambitious effort to sequence all 60,000 species believed to be on the British Isles over the next 12 years in this presentation at the PAG 2020 Conference. The Sanger team has already generated data for 94 species, including 44 new moth and butterfly (Lepidoptera) PacBio assemblies, which Blaxter describes in this presentation.
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 a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.
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.
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…
In this SMRT Leiden 2020 Online Virtual Event presentation, Marcela Uliano da Silva of Wellcome Sanger Institute shares her work using CCS data combined with HiC reads to assemble chromosome-level genomes for Lepidoptera. This was done as part of the The Darwin Tree of Life Project which is assembling high-quality genomes for all eukaryotic species in Britain and Ireland. Find data: https://github.com/darwintreeoflife/darwintreeoflife.data
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 resource for primary and applied research across the tree of life. Genome projects for small-bodied, non-model organisms such as insects face several unique challenges including limited DNA input quantities, high heterozygosity, and difficulty of culturing or inbreeding in the lab. Recent progress in PacBio library preparation protocols, sequencing throughput, and read accuracy address these challenges. We present several case studies including the Red Admiral (Vanessa atalanta), Monarch Butterfly (Danaus plexippus), and Anopheles malaria mosquitoes that highlight the benefits of sequencing single individuals for de novo genome assembly projects, and the ease at which…