Training
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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.
Structural Variant Calling Analysis Application
PacBio RS II, 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: =50 bp) insertions and deletions in a sample relative to a reference from whole genome sequence data. This tutorial covers features of SMRT Link v5.0.0.
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.
Circular Consensus Sequence Analysis Application
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an overview of the Circular Consensus Sequence (CCS) analysis application. The CCS algorithm is used in applications that require distinguishing closely related DNA molecules in the same sample. Applications of CCS include profiling microbial communities, resolving viral populations and accurately identifying somatic variations within heterogeneous tumor cells. This tutorial covers features of SMRT Link v5.0.0.
HGAP4 De Novo Assembly Application
PacBio RS II, Sequel System
Analysis
Description +
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.
Iso-Seq Analysis Application
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an overview of the Isoform Sequencing (Iso-Seq) analysis application. The Iso-Seq application provides reads that span entire transcript isoforms, from the 5' end to the 3' polyA-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 v5.0.0.
Long Amplicon Analysis Application
PacBio RS II, Sequel System
Analysis
Description +
This tutorial provides an overview of the Long Amplicon Analysis (LAA) application. The LAA algorithm generates highly accurate, phased and full-length consensus sequences from long amplicons. Applications of LAA include HLA typing, alternative haplotyping, and localized de novo assemblies of targeted genes. This tutorial covers features of SMRT Link v5.0.0.
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.
Using the Integrative Genomics Viewer (IGV) to Visualize PacBio Long-read SMRT Sequencing Data
PacBio RS II, Sequel System
Analysis
Description +
In this video, PacBio scientists present ongoing improvements to the Integrative Genomics Viewer (IGV) and demonstrate how multiple new features improve visualization support for PacBio long-read sequencing data. The video describes these recent updates which include; quick consensus accuracy mode to hide random single-molecule errors, direct phasing of haplotypes using long-read evidence, and visual annotation of insertions and deletions relative to the reference with enumeration of gap size for individual reads. These new features are available now in the development version of IGV, which can be found at http://software.broadinstitute.org/software/igv/download_snapshot. The Sequel sequencing data used in this demonstration is also publicly available here https://www.pacb.com/blog/identifying-structural-variants-na12878-low-fold-coverage-sequencing-pacbio-sequel-system/.
Introduction to SMRT Sequencing
PacBio RS II, Sequel System
Sequencing
Description +
A brief animated introduction to Pacific Biosciences' Single Molecule, Real-Time (SMRT) Sequencing, including the SMRT Cell and ZMW (zero mode waveguide).