Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.
Accurate sequencing data is key for University of Florida scientist Ana Conesa. She is using PacBio HiFi reads from the Sequel II System to identity alternative isoforms and determine the functional impact of different isoform expression in her transcriptome research.
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.
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, 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
The Earlham Institute was one of the first labs to adopt the PacBio Sequel II System. Karim Gharbi, Head of Genomics Pipelines, discusses how SMRT Sequencing and HiFi reads have increased throughput and reduced costs for genome, transcriptome, and metagenomics projects.
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.
Jeremy Schmutz discusses the increased throughput and reduced project costs using HiFi reads from the PacBio Sequel II System in his work sequencing, assembling, and analyzing a variety of genomes at the HudsonAlpha Institute for Biotechnology.
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.
Highly accurate long reads, known as HiFi reads, are a new tool in scientists’ sequencing toolbox. Hear PacBio users share how they are using HiFi reads to explore the genomes, transcriptomes, metagenomes and the benefits HiFi reads provide for their addressing critical life science questions.
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.