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Friday, February 5, 2021

Webinar: Beginner’s guide to PacBio SMRT Sequencing data analysis

PacBio SMRT Sequencing is fast changing the genomics space with its long reads and high consensus sequence accuracy, providing the most comprehensive view of the genome and transcriptome. In this webinar, I will talk about the various data analysis tools available in PacBio’s data analysis suite – SMRT Link – as well as 3rd party tools available. Key applications addressed in this talk are: Genome Assemblies, Structural Variant Analysis, Long Amplicon and Targeted Sequencing, Barcoding Strategies, Iso-Seq Analysis for Full-length Transcript Sequencing

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Friday, February 5, 2021

Webinar: Chasing alternative splicing in cancer: Simplified full-length isoform sequencing

Tremendous flexibility is maintained in the human proteome via alternative splicing, and cancer genomes often subvert this flexibility to promote survival. Identification and annotation of cancer-specific mRNA isoforms is critical to understanding how mutations in the genome affect the biology of cancer cells. While microarrays and other NGS-based methods have become useful for studying transcriptomes, these technologies yield short, fragmented transcripts that remain a challenge for accurate, complete reconstruction of splice variants. The Iso-Seq method developed at PacBio offers the only solution for direct sequencing of full-length, single-molecule cDNA sequences needed to discover biomarkers for early detection and cancer stratification,…

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Friday, February 5, 2021

Webinar: SMRT Sequencing applications in plant and animal sciences: an overview

In this webinar, Emily Hatas of PacBio shares information about the applications and benefits of SMRT Sequencing in plant and animal biology, agriculture, and industrial research fields. This session contains an overview of several applications: whole-genome sequencing for de novo assembly; transcript isoform sequencing (Iso-Seq) method for genome annotation; targeted sequencing solutions; and metagenomics and microbial interactions. High-level workflows and best practices are discussed for key applications.

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Friday, February 5, 2021

Webinar: A sketch of assembly recipes for PacBio data

This webinar, presented by Nisha Pillai, provides an overview of bioinformatics approaches for PacBio Single Molecule, Real-Time (SMRT) Sequencing data and discusses the whole genome sequencing application including: assembly workflow designs, an overview analysis tools for de novo assembly of SMRT Sequencing data (HGAP4, FALCON & FALCON-Unzip), and finally best practices and case studies.

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Friday, February 5, 2021

PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through Iso-seq analysis

In this PAG 2018 presentation, John Williams of University of Adelaide, presents research on using PacBio SMRT Sequencing to explore the genetic origins of cattle subspecies, Angus (Bos taurus taurus) and Brahman (Bos taurus indicus). He shares RNA sequencing data using the PacBio Iso-Seq method to compare transcriptomes and phase allelic expression and describes how the IsoPhase technique enables evaluation of SNPs through transcriptome mapping back to the single genome of a cross-bred individual. Using a genomic and transcriptomic approach, two high-quality genomes from a single individual and gene isoforms specific to each subspecies are being identified.

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Friday, February 5, 2021

Webinar: Using Iso-Seq analysis to build a better annotation

Long-read sequencing technologies like Iso-Seq analysis present researchers with a powerful tool for probing the transcriptomes of many species. The ability to sequence transcripts from end-to-end has revealed transcription complexity on a scale that was previously impossible. This sequence rich information has also improved our ability to predict transcript functions and biotypes. Researchers can now use Iso-Seq analysis to discover transcript models in almost any species with an accuracy on par with human and mouse annotations. In this webinar, Richard Kuo discusses the core concepts behind Iso-Seq analysis and how to use it to improve or build a new transcriptome…

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Friday, February 5, 2021

Educational Video: Step 1 – from sample to sequencing data for de novo assembly

This video provides an overview of the techniques and steps of preparing samples, DNA, and libraries for PacBio Single Molecule, Real-Time (SMRT) Sequencing to be used in de novo assembly projects. In this video, a PacBio scientist covers how to assess DNA quantity and purity, size-selection of DNA libraries, and provides and introduction to SMRT Sequencing, including the benefits of long-reads when generating high-quality genome assemblies.

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Friday, February 5, 2021

Educational Video: Step 2 – de novo assembly of a genome

This video provides an overview of the techniques and steps of generating a de novo genome assembly with long-read sequencing data generated using PacBio Single Molecule, Real-Time (SMRT) Sequencing. In this video, a PacBio scientist covers the benefits of long reads when generating high-quality genome assemblies, the latest tools for creating assemblies, including HGAP, FALCON and FALCON-Unzip, how to polish and assess the quality of a genome assembly, and how to submit an assembly to NCBI.

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Friday, February 5, 2021

Webinar: Assembling high-quality human reference genomes for global populations

This webinar highlights global initiatives currently underway to use Single Molecule, Real-Time (SMRT) Sequencing to de novo assemble genomes of individuals representing multiple ethnic populations, thereby extending the diversity of available human reference genomes. In their presentations, Tina Graves-Lindsay from Washington University and Adam Ameur from Uppsala University spoke about diploid assemblies, discovering novel sequence and improving diversity of the current human reference genome. Finally, Paul Peluso of PacBio presented data from the recent effort to sequence a Puerto Rican genome and shared a SMRT Sequencing technology roadmap showing the next several upgrades for the Sequel System.

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Friday, February 5, 2021

Webinar: Survey of transcriptome diversity using Iso-Seq analysis

The Iso-Seq method enables the sequencing of transcript isoforms from the 5’ end to their poly-A tails, eliminating the need for transcript reconstruction and inference. This webinar provides a comprehensive guide to Iso-Seq method data analysis, bioinformatics, and review key applications.

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Friday, February 5, 2021

User Group Meeting: The trials and tribulations of high quality human genome assembly

In this PacBio User Group Meeting presentation, Tina Graves-Lindsay of the McDonnell Genome Institute and the Genome Reference Consortium speaks about the importance of phasing human reference genomes. Her team is now working on its fifteenth human genome assembly — part of a major effort to improve genomic representation of ethnic diversity — with a pipeline that generates 60-fold PacBio coverage for a de novo assembly, followed by scaffolding with other technologies. They are also using FALCON-Unzip to separate haplotypes, leading to reference-grade diploid assemblies. This approach has already helped resolve errors seen in other genomes and even the gold-standard…

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Friday, February 5, 2021

User Group Meeting: Development, validation, and applications of a high-fidelity, species-specific, eubacterial pan-domain microbiome assay on the PacBio System

In this PacBio User Group Meeting presentation, Garth Ehrlich of Drexel University College of Medicine shares his work on developing a microbiome assay that uses SMRT Sequencing to provide high-quality coverage of the 16S bacterial rRNA for species identification. The microbiome analysis pipeline, MCSMRT, takes advantage of PacBio circular consensus sequencing (CCS) technology and second-generation pathway analysis system for generating extremely high-fidelity sequences that provide the user with ultra-high-confidence species-level microbiome data.

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