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Wednesday, January 6, 2021

Tutorial: HGAP4 de novo assembly application [SMRT Link v5.0.0]

This tutorial provides an overview of the Hierarchical Genome Assembly Process (HGAP4) de novo assembly analysis application. HGAP4 generates accurate de novo assemblies using only PacBio data. HGAP4 is suitable for assembling a wide range of genome sizes and complexity. HGAP4 now includes some support for diploid-aware assembly. This tutorial covers features of SMRT Link v5.0.0.

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Wednesday, January 6, 2021

Webinar: Complete genomes within reach – Closing bacterial genomes from the lakes of Minnesota to NYC hospitals

In this webinar, Ben Auch, Research Scientist, Innovation Lab, University of Minnesota Genomics Center, Cody Sheik, Assistant Professor of Biology, University of Minnesota Duluth, and Harm van Bakel, Assistant Professor of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai provide details of the newly updated microbial whole genome sequencing pipeline, which leverages the multiplexing capabilities of the Sequel System, share new insights into the ecophysiology of Minnesota microbes using long-read sequencing, and show of how whole genome sequencing is used in pathogen surveillance programs at hospitals.

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Wednesday, January 6, 2021

User Group Meeting: Sequencing chemistry & application updates

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.

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Wednesday, January 6, 2021

User Group Meeting: No Assembly Required – Making the most of Iso-Seq data

In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.

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Wednesday, January 6, 2021

Webinar: Sequence with Confidence – Introducing the Sequel II System

In this webinar, Jonas Korlach, Chief Scientific Officer, PacBio provides an overview of the features and the advantages of the new Sequel II System. Kiran Garimella, Senior Computational Scientist, Broad Institute of MIT and Harvard University, describes his work sequencing humans with HiFi reads enabling discovery of structural variants undetectable in short reads. Luke Tallon, Scientific Director, Genomics Resource Center, Institute for Genome Sciences, University of Maryland School of Medicine, covers the GRC’s work on bacterial multiplexing, 16S microbiome profiling, and shotgun metagenomics. Finally, Shane McCarthy, Senior Research Associate, University of Cambridge, focuses on the scaling and affordability of high-quality…

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Wednesday, January 6, 2021

SMRT Leiden: Cas9 off-target sequencing and analysis

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.

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Wednesday, January 6, 2021

SMRT Leiden: Epigenomics in the ERA of third-generation sequencing: A large-scale study of the human pathogen Clostridioides difficile

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.

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Wednesday, January 6, 2021

SMRT Leiden: Calling all variants with HiFi reads

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.

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Wednesday, January 6, 2021

SMRT Leiden: The functional iso-transcriptomics pipeline: from long reads to biological insights

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.

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Wednesday, January 6, 2021

SMRT Leiden: Improved phased assembly using HiFi 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.

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