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 Pedro Oliveira of Mount Sinai shares his research on Clostridioides – a leading cause of nosocomial-acquired diarrhea and colitis across the developed world. In this study, Oliveira and coworkers performed the first comprehensive DNA methylome analysis of 36 human C. difficile isolates from a hospital setting using SMRT Sequencing and comparative epigenomics.
In this SMRT Leiden 2020 Online Virtual Event presentation, William Rowell of PacBio shares work on using HiFi reads – which combine the length of traditional long reads with the accuracy of short reads, making them great for comprehensive variant detection. This presentation covers the recommended workflows for detecting both small variants and structural variants from HiFi reads.
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.
Studying microbial genomics and infectious disease? Learn how the PacBio Sequel II System can help advance your research, with first-hand perspectives from scientists who are investigating SARS-CoV-2 and COVID-19. In this webinar, Melissa Laird-Smith (Mt. Sinai School of Medicine) discusses her work evaluating the impact of host immune restriction in health and disease with high resolution HLA typing. She is joined by Corey Watson (University of Louisville School of Medicine) who talks about overcoming complexity to elucidate the role of IGH haplotype diversity in antibody-mediated immunity. Hosted by Meredith Ashby, Director of Microbial Genomics at PacBio. Access additional PacBio resources…
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.
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.
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.
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…