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Sunday, October 25, 2020

AGBT Conference: Automated de novo genome assemblies and bacterial epigenomes using PacBio sequencing

In this AGBT plenary talk, Jonas Korlach presented a number of collaborative studies between PacBio and other institutions to make use of highly accurate, long-read sequence data, which has led to a revival of finished genomes. Examples from the infectious disease or pathogen realm included Pertussis, Salmonella, and Listeria, all of which now have closed genomes from PacBio-generated data. Korlach also reported on epigenomic information in Salmonella and Listeria, indicating potential new forms of DNA modifications.

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Sunday, October 25, 2020

Customer Experience: Sequencing through GC-rich microbial genomes with the high-accuracy PacBio RS

The Genome Analysis Centre’s (TGAC) Matthew Clark, who leads the sequencing technology development group, says that high-accuracy PacBio sequencing is ideal for GC-rich or AT-rich genomes since it shows no GC bias. This has enabled his team to sequence several strains of Streptomyces and elucidate gene clusters thought to be important in antibiotic production. Clark says long reads from SMRT Sequencing are good for other hard-to-sequence regions, such as repeats or large transposable elements.

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Sunday, October 25, 2020

PAG Conference: From sequencing to chromosomes – new de novo assembly and scaffolding methods improve the goat reference genome

Sergey Koren of the National Biodefense Analysis and Countermeasures Center (NBACC) discusses integrating the MinHash Alignment Process (MHAP) with Celera Assembler to enable reference-grade assemblies of model organisms, revealing novel heterochromatic sequences and filling low-complexity gap sequences in the GRCh38 human reference genome. Dr. Koren and his team have applied this method to assemble the San Clemente goat genome. Combining SMRT Sequencing and next-generation optical mapping from BioNano Genomics generates an assembly that is over 150-fold more contiguous than the latest Capra hircusgoat reference. In combination with Hi-C sequencing, the assembly surpasses reference assemblies de novo, with minimal manual intervention.…

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Sunday, October 25, 2020

PAG Conference: Analysis of structural variants using 3rd generation sequencing

Michael Schatz of Cold Spring Harbor Laboratory and Johns Hopkins University discusses the challenges in detecting structural variations (SVs) in high throughput sequencing data, especially more complex SVs such as a duplication nested within an inversion. To overcome these challenges, Dr. Schatz and his team have been applying long-read sequencing to analyze SVs in a range of samples from small microbial genomes, through mid-sized plant and animal genomes, to large mammalian genomes. The increased read lengths, which currently average over 10kbp and some approach 100kbp, make it possible to span more complex SVs and accurately assess SVs in repetitive regions,…

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Sunday, October 25, 2020

Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries

In this Webinar, we will give an introduction to Pacific Biosciences’ single molecule, real-time (SMRT) sequencing. After showing how the system works, we will discuss the main features of the technology with an emphasis on the difference between systematic error and random error and how SMRT sequencing produces better consensus accuracy than other systems. Following this, we will discuss several ground-breaking discoveries in medical science that were made possible by the longs reads and high accuracy of SMRT Sequencing.

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Sunday, October 25, 2020

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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Sunday, October 25, 2020

User Group Meeting: Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System

In this PacBio User Group Meeting presentation, PacBio scientist Meredith Ashby shared several examples of analysis — from full-length 16S sequencing to shotgun sequencing — showing how SMRT Sequencing enables accurate representation for metagenomics and microbiome characterization, in some cases even without fully assembling genomes. New updates will provide users with a dedicated microbial assembly pipeline, optimized for all classes of bacteria, as well as increased multiplexing on the Sequel II System, now with 48 validated barcoded adapters. That throughput could reduce the cost of microbial analysis substantially.

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Sunday, October 25, 2020

Webinar: Bioinformatics lunch & learn – Better assemblies of bacterial genomes and plasmids with the new microbial assembly pipeline in SMRT Link v8.0

Microbial Assembly is our latest pipeline, specifically designed to assemble bacterial genomes (between 2 and 10 Mb) and plasmids. This pipeline includes the implementation of a new, circular-aware read alignment tool (Raptor), among other algorithmic improvements, which will be covered in this webinar. The topics covered include, staged assembly of bacterial chromosomes and plasmids, implementation of Raptor, a circular-aware read aligner, himeric read detection, origin of replication orientation, troubleshooting and more.

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Sunday, October 25, 2020

Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing

Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…

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Wednesday, October 21, 2020

Product Note: SMRTbell express template prep 2.0 for large-insert libraries

The SMRTbell Express Template Prep Kit 2.0 provides a streamlined, single-tube reaction strategy to generate SMRTbell libraries from 500 bp to >50 kb insert size targets to support large-insert genomic libraries, multiplexed microbial genomes and amplicon sequencing. With this new formulation, we have increased both the yield and efficiency of SMRTbell library preparation for SMRT Sequencing while further minimizing handling-induced DNA damage to retain the integrity of genomic DNA (gDNA). This product note highlights the key benefits, performance, and resources available for supporting de novo genome sequencing and structural variant detection projects. Our large-insert gDNA protocol has been streamlined to…

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Wednesday, October 21, 2020

Product Note: SMRTbell express template prep 2.0 for microbial multiplexing

The SMRTbell Express Template Prep Kit 2.0 provides a streamlined, single-tube reaction strategy to generate SMRTbell libraries from 500 bp to >50 kb insert size targets to support large-insert genomic libraries, multiplexed microbial genomes and amplicon sequencing. With this new formulation, we have increased both the yield and efficiency of SMRTbell library preparation for SMRT Sequencing while further minimizing handling-induced DNA damage to retain the integrity of genomic DNA (gDNA). This product note highlights the key benefits, performance, and resources available for obtaining complete microbial genome assemblies with multiplexed sequencing. By using a single-tube, addition-only strategy, the streamlined workflow reduces…

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Wednesday, October 21, 2020

Application Note: Microbial multiplexing workflow on the Sequel System

Obtaining microbial genomes with the highest accuracy and contiguity is extremely important when exploring the functional impact of genetic and epigenetic variants on a genome-wide scale. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism. SMRT Sequencing provides complete genomes, often assembled into a single contig. Our streamlined microbial multiplexing procedure for the Sequel System, from library preparation to genome assembly, can be completed with less than 8 hours bench time. Starting with high-quality genomic DNA (gDNA),…

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