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AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector

Neafsey, Daniel
Broad Institute

2017

Description +

At AGBT 2017, the Broad Institute’s Daniel Neafsey reported a large collaborative effort to sequence the mosquito that carries Zika virus. The team is using long-read PacBio sequencing to produce a high-quality genome assembly, which Neafsey expects will replace the 10-year-old Sanger assembly for Aedes aegypti. The new assembly reduces the number of contigs by at least 10-fold, boosts the contig N50 to nearly 2 Mb, and features more complete gene content.

AGBT PacBio Workshop: De novo sequencing of the naked mole rat genome

Roy, Margaret
Calico Life Sciences

2017

Description +

At AGBT 2017, Margaret Roy from Calico Life Sciences discussed a de novo genome sequencing effort for the naked mole rat. This animal has a remarkably long life span and resistance to cancer, both of which make it interesting for studies of life extension. The team is using SMRT Sequencing for a more complete, contiguous assembly than the two existing short-read-based assemblies. Included: data from the Sequel System.

AGBT PacBio Workshop: High-throughput HLA class I whole gene and HLA class II long range typing on PacBio RSII and Sequel Platforms

Cereb, Nezih
Histogenetics

2017

Description +

In a talk at AGBT 2017, Histogenetics CEO Nezih Cereb reported on how SMRT Sequencing is allowing his team to produce full-length, phased sequences for HLA alleles, which are important for matching organ transplants to recipients. The company is typing thousands of samples per day on their PacBio RS II systems and their new Sequel System. Cereb noted that SMRT Sequencing is unique in its ability to reliably phase mutations in the HLA alleles without imputation. Cereb concluded with his plans to use this approach for other complex regions, such as KIR, and announced their continued increasing HLA typing capacity due to Histogenetic’s acquisition of three additional Sequel Systems.

AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs

Korlach, Jonas
PacBio

2017

Description +

In this AGBT 2017 talk, PacBio CSO Jonas Korlach provided a technology roadmap for the Sequel System, including plans the continue performance and throughput increases through early 2019. Per SMRT Cell throughput of the Sequel System is expected to double this year and again next year. Together with a new higher-capacity SMRT Cell expected to be released by the end of 2018, these improvements result in a ~30-fold increase or ~150 Gb / SMRT Cell allowing a real $1000 real de novo human genome assembly. Also discussed: Additional application protocol improvements, new chemistry and software updates, and a look at recent studies featuring SMRT Sequencing.

AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples

Schatz, Michael
John Hopkins University

2017

Description +

At AGBT 2017, Mike Schatz from Johns Hopkins University and Cold Spring Harbor Laboratory presented data from sequencing, assembling, and analyzing personalized, phased diploid genomes with either Illumina, 10x Genomics, and PacBio SMRT Sequencing. Compared to the short-read-based methods, PacBio data assembled in large, complete contigs and contained the broadest range of structural variants with the best resolution. Plus: unexpected translocation findings with SMRT Sequencing, validated in follow-up studies.

Tutorial: Base Modification Detection, Base Modification and Motif Analysis Application


PacBio

2017

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.

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.

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.

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.

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.

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.

Tutorial: SMRT Link Overview


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.

PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies

Jarvis, Erich
Rockefeller University

2017

Description +

At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing and scaffolding technologies. Analyses include gene content, error rate, chromosome metrics, and more. Plus: a long-read look at four genes associated with vocal learning.

PAG PacBio Workshop: De novo sequencing of the koala genome

Johnson, Rebecca
Australian Museum Research Institute

2017

Description +

In this talk at the Plant and Animal Genome Conference in 2017, Rebecca Johnson from the Australian Museum Research Institute describes how long-read PacBio sequencing generated the most complete assembly yet for the koala genome. Among the findings: novel genes involved in lactation and natural antimicrobials that show effectiveness against drug-resistant bacteria. The new assembly is especially important for koala conservation efforts.

PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti

Matthews, Ben
HHMI and Rockefeller University

2017

Description +

In this PAG 2017 presentation, Ben Matthews describes a new genome assembly for Aedes aegypti, the mosquito responsible for spreading Zika virus, yellow fever, and other infectious diseases. By using PacBio long-read sequencing, scientists produced an assembly that is much more complete and contiguous than a previous assembly; 7,500 transcripts map to the new contigs but not to the old assembly. The genome is important for designing guide RNAs for CRISPR, understanding resistance to mosquito repellants, and much more.

Event

SMRT Leiden Conferences

May 2 - May 4, 2017

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