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…
In this SMRT Leiden 2020 Online Virtual Event presentation, Ana Conesa of the University of Florida shares her work on the latest updates to the Funciitonal Iso-Annot software, that includes SQANTI, IsoAnnot and tappAS. SQANTI includes new features such as assessment of TSS and TTS sites and sequencing depth. SQANTI3 includes direct annotation of IsoAnnot annotation labels and direct compatibility with tappAS for differential splicing analysis and functional annotation of long reads data.
In this SMRT Leiden 2020 Online Virtual Event presentation, Ivan Sovic of PacBio shares work on a new tool for improved and phased assembly of HiFi data called IPA. IPA delivers highly accurate and contiguous phased assemblies at very high speeds – it can assemble, phase and polish a 34x human genome dataset in just 14 hours on a single 80 core machine, with the final base quality >Q50. IPA constructs true haplotigs through a dedicated phasing process resulting in high phasing accuracy and haplotype separation of the assembly, as well as very high BUSCO gene completeness scores.
In this SMRT Leiden 2020 Online Virtual Event presentation, Erwin Datema of KeyGene shares his work on using high-throughput, accurate long-read sequencing technologies, such as PacBio HiFi sequencing, to drastically reduced the investment required to generate high-quality genome sequences. As a result, they have shifted away from the reference-centric view of the genome, and entered the pan-genome era. Here, Datema highlights some of the breakthrough algorithmic innovations KeyGene has developed to generate and analyze population-scale pan-genomes for plant genomes of all complexities and sizes.
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 SMRT Leiden 2020 Online Virtual Event presentation, Erich Jarvis of Rockefeller University shares an update on the Vertebrate Genome Project and a few exciting developments related to using the new Platinum-quality genomes to study functional evolutionary traits.
In this SMRT Leiden 2020 Online Virtual Event presentation, Richard Kuo of The Roslin Institute shares his work on using Iso-Seq data to gain a better understanding of the biology of a species. Kuo demonstrates how these analyses can change the way we look at genome assemblies, differential gene expression, and functional annotation.
Richard Kuo’s research at the Roslin Institute exploring non-coding RNA of avian species requires high accuracy. SMRT Sequencing on the PacBio Sequel II System and the Iso-Seq method have given him confidence in annotations across entire genomes and transcriptomes.
In this SMRT Leiden 2020 Online Virtual Event presentation, Ida Hoijer of Uppsala University shares her research on developing a long-read sequencing-based method for detection of CRISPR-Cas9 off-target effects, along with a customized analysis pipeline. By applying an off-target sequencing (OTS) method on a human embryonic cell line, they detected 55 on- and off-target sites for three different gRNAs, including allele-specific off-targets. As the OTS approach finds off-targets that are difficult to predict using in silico or short-read based methods, it may become an important tool for genome editing.
En este seminario online Carmen Guarco, Senior Field Application Scientist especializada en Bioinformática en PacBio, ofrece una introducción a la tecnología de secuenciación SMRT, las secuencias HiFi y sus aplicaciones incluyendo el ensamblaje de genomas y la secuenciación de ARN. Álvaro G. Hernandez, Director de la Unidad de Secuenciación de ADN en la Universidad de Illinois at Urbana-Champaign, ofrece recomendaciones para asegurar que la secuenciación de genomas sea de alta calidad con ejemplos de parámetros que definen una buena secuenciación. Además, cubre los beneficios de secuenciación del gen 16S en comparación con secuenciación de regiones variables con ejemplos de la…
In this ASHG 2020 PacBio Workshop Hagen Tilgner of Cornell University shares how he has used single-cell RNA sequencing using long reads to identify novel isoform expression in brain tissues.
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.
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.
In this webinar, scientists from PacBio share how using Single Molecule, Real-Time (SMRT) Sequencing, you can generate highly accurate long reads – HiFi reads – with 99% accuracy (Q20) and read lengths of 10 kb or more. This high resolution of each single molecule enables species or strain-level profiling of complex populations in both targeted and shotgun sequencing experiments. Genome assemblies are more cost effective than ever before when sequencing metagenomics samples with the Sequel II System.
Background: Long-read sequencing presents several potential advantages for providing more complete gene profiling of metagenomic samples. Long reads can capture multiple genes in a single read, and longer reads typically result in assemblies with better contiguity, especially for higher abundance organisms. However, a major challenge with using long reads has been the higher cost per base, which may lead to insufficient coverage of low-abundance species. Additionally, lower single-pass accuracy can make gene discovery for low-abundance organisms difficult. Methods: To evaluate the pros and cons of long reads for metagenomics, we directly compared PacBio and Illumina sequencing on a soil-derived sample,…