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SMRTLink-CCS-thumb

Tutorial: Circular Consensus Sequence analysis application


PacBio

2017

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.

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Tutorial: HGAP4 de novo assembly application


PacBio

2017

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.

SMRTLink-Iso-Seq

Tutorial: Iso-Seq analysis application


PacBio

2017

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.

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Tutorial: Long Amplicon Analysis application


PacBio

2017

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.

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Tutorial: Overview of SMRT Link


PacBio

2017

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.

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Tutorial: SMRT Analysis Overview


PacBio

2017

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.

AGBT Conference: Addressing complex disease and hidden heritability with the Sequel System

Korlach, Jonas
PacBio

2016

Description +

Jonas Korlach presents data from the new Sequel System and discussed the value of SMRT Sequencing for addressing complex disease. He shows comparisons of Sequel data to PacBio RS II data in applications such as targeted sequencing of structural variants, somatic variation detection of cancer samples, and full-length isoform transcript sequencing.

AGBT Conference: Evolving approaches to reference assembly improvement

Schneider, Valerie
National Center for Biotechnology Information

2016

Description +

Valerie Schneider speaks about Genome Reference Consortium efforts to improve assembly of the human reference genome. SMRT Sequencing has been useful for resolving some highly repetitive regions, like the mucin genes. Haploid assemblies produced with long-read sequencing are also making complex regions more tractable.

AGBT Conference: Long-read sequence of the gorilla genome

Hill, Christopher
University of Washington

2016

Description +

Christopher Hill presents data from efforts to produce reference-grade assemblies for the great ape species. Using SMRT Sequencing, Hill and his colleagues are generating assemblies with much higher contiguity to resolve repetitive and other particularly complex regions. In this talk, he focuses on data from their new high-quality gorilla assembly.

AGBT Conference: The first African reference genome assembly

Meltz Steinberg, Karyn
McDonnell Genome Institute, Washington University in St. Louis

2016

Description +

Karyn Meltz Steinberg presents the first high quality African reference genome assembly of the Yoruban individual, NA19240, produced from SMRT Sequencing data. She said PacBio sequencing offers significant improvement over short-read sequence data for high-quality assemblies.

AGBT Roche and PacBio Workshop: Closing remarks

Korlach, Jonas
PacBio

2016

Description +

In his closing remarks, PacBio CSO Jonas Korlach comments on the trends of whole genome sequencing, and the recognition of the need for higher-quality human genome assemblies. He also demonstrated that long-read sequencing allows scientists to find SNPs and structural variants while also analyzing epigenetics and phasing genes or variants.

AGBT Roche and PacBio Workshop: Leveraging SMRT Sequencing technology for developing niche assays with diagnostic potential

Sebra, Robert
Icahn School of Medicine at Mount Sinai

2016

Description +

Robert Sebra reports the use of SMRT Sequencing at the Icahn Institute and presents some early data from the new Sequel System. Topics include: Targeted sequencing applications for CYP2D6 metabolism and Gaucher disease, tandem repeat detection in FTD/ALS patients, structural variation detection for Goldenhar Syndrome, inverted PCR assays for detection of DNA damage in Glioblastome, whole gene BRCA sequencing, and sensitive somatic variant detection in heterogeneous tissues.