Training
Welcome to the PacBio training page. Here, you can search for and download online webinars, e-Modules, and other training documents. If you have any questions about our training materials, please contact us.
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Best Practices for Working with PacBio Tools (SMRT Link & Developmental) on the Command Line
Sequel II System, Sequel System
Analysis
Description +
This webinar, presented by Roberto Lleras, provides the best practices for working with PacBio tools (SMRT Link and Developmental) on the command line. Please access this file for step-by-step instructions for installing SMRT Analysis tools and pbbioconda in order to analyze SMRT Sequencing data on the command line: https://www.pacb.com/wp-content/uploads/Bioinformatics-Webinar-Session-1-Getting-Started.pdf
Sequel II System v7.0 & SMRT Link v7.0 Overview
Sequel II System
Analysis, Binding, Sample Preparation, Sequencing, Template Preparation
Description +
This technical training presentation provides an overview of key features & benefits of the Sequel II System v7.0.0 and SMRT Link v7.0.0. 'Best Practices' overviews for sample library preparation and sequencing are also presented for whole genome sequencing for de novo assembly of large genomes, whole genome sequencing for structural variation detection, and human variant detection applications.
SMRTbell Library Preparation for High Fidelity (HiFi/CCS) Long Read Sequencing
Sequel II System, Sequel System
Binding, Sample Preparation, Sequencing, Template Preparation
Description +
This technical training presentation provides an overview of HiFi long read sequencing features & applications and summarizes HiFi library sample preparation & sequencing workflow details, HiFi long read sequencing performance example data (Sequel II System), and variant detection application best practices.
SMRTbell Express Template Prep Kit 2.0: Low DNA Input Library Preparation
Sequel II System, Sequel System
Binding, Sample Preparation, Sequencing, Template Preparation
Description +
This technical training presentation provides an overview of the low DNA input workflow and summarizes experimental design considerations, low DNA input sample QC requirements, low DNA input sample preparation & sequencing workflow details, and low DNA input library example performance data (Sequel System 6.0 / Chemistry 3.0). General recommendations for high-molecular weight gDNA QC and handling for SMRTbell library construction are also presented.
SMRTbell Express Template Prep Kit 2.0: Multiplexed Microbial Library Preparation
Sequel II System, Sequel System
Analysis, Binding, Sample Preparation, Sequencing, Template Preparation
Description +
This technical training presentation summarizes key features & benefits, new reagents & consumables and kit configuration information for the SMRTbell Express Template Preparation Kit 2.0 product and describes multiplexed microbial sample preparation & sequencing workflow details, multiplexed microbial data analysis workflow details, and multiplexed microbial library example performance data (Sequel System v6.0 / Chemistry v3.0). General recommendations for high-molecular weight gDNA QC and handling for SMRTbell library construction are also presented.
SMRTbell Express Template Prep Kit 2.0: Large Insert Genomic Library Preparation
Sequel II System, Sequel System
Binding, Sample Preparation, Sequencing, Template Preparation
Description +
This technical training presentation summarizes key features & benefits, new reagents & consumables and kit configuration information for the SMRTbell Express Template Preparation Kit 2.0 product and describes supported large insert gDNA library types & sample input requirements, large insert library sample preparation & sequencing workflow details and large insert library example performance Data (Sequel System 6.0 / Chemistry 3.0). General recommendations for high-molecular weight gDNA QC, shearing and handling for SMRTbell library construction are also presented.
Iso-Seq Analysis Application [SMRT Link v6.0.0]
Sequel System
Analysis
Description +
This tutorial provides an overview of the Isoform Sequence (Iso-Seq) analysis application. The Iso-Seq application provides reads that span entire transcript isoforms, from the 5' end to the 3' poly A-tail. Generation of accurate, full-length transcript sequences greatly simplifies analysis by eliminating the need for transcript reconstruction to infer isoforms using error-prone assembly of short RNA-seq reads. This tutorial covers features of SMRT Link v6.0.0.
Structural Variant Calling [SMRT Link v6.0.0]
Sequel System
Analysis
Description +
This tutorial provides an overview of the Structural Variant Calling application in SMRT Link and a live demo of how to launch an analysis in SMRT Link and interpret the results. This application identifies large (default: = 20 bp) insertions, deletions, inversions and translocations in a sample relative to a reference from.This tutorial covers features of SMRT Link v6.0.0.
Step 2 – De Novo Assembly of a Genome
PacBio RS II, Sequel System
Analysis
Description +
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.
Step 1 – From Sample to Sequencing Data for De Novo Assembly
PacBio RS II, Sequel System
Binding, Sequencing, Template Preparation
Description +
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.
Multiplexed Microbial Assembly in SMRT Link v5.1.0
Sequel System
Analysis
Description +
This tutorial provides an overview of the PacBio Demultiplex Barcodes analysis application in SMRT Link, followed by de novo assembly of the demultiplexed samples using HGAP4 for the Multiplexed Microbial Assembly analysis application. This tutorial covers features of SMRT Link v5.1.0.
Minor Variant Analysis Application
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an overview of the Minor Variants Analysis application in SMRT Link and a live demo of how to launch an analysis in SMRT Link and interpret the results. This application identifies and phases minor single nucleotide variants in complex populations.
SMRT Link Overview
PacBio RS II, Sequel System
Analysis, Sequencing
Description +
This tutorial provides a high-level overview of the features contained within the SMRT Link software. SMRT Link is the web-based end-to-end software workflow manager for run design and set-up on the Sequel System, Data Management, and SMRT Analysis.
Base Modification Detection, Base Modification and Motif Analysis Application
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an overview of the Base Modification and Motif analysis application for identifying common bacterial epigenetic modifications and analyzing methyltransferase recognition motifs. SMRT Analysis software supports epigenetic research by measuring the rate of DNA base incorporation during Single Molecule, Real-Time Sequencing. This tutorial covers features of SMRT Link v5.0.0.
SMRT Analysis Overview and Resequencing
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an introduction to SMRT Analysis within SMRT Link. The training includes an overview of the various PacBio analysis applications and an introduction on their use. This tutorial covers features of SMRT Link v5.0.0.