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Thursday, January 7, 2021

Case Study: Pioneering a pan-genome reference collection

At DuPont Pioneer, DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in commercial crops such as maize, soybean, sorghum, sunflower, alfalfa, canola, wheat, rice, and others. They cannot afford to wait the years it has historically taken for high-quality reference genomes to be produced. Nor can they rely on a single reference to represent the genetic diversity in its germplasm.

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Thursday, January 7, 2021

Product Note: Fast, high-resolution DNA sizing with the Agilent Femto Pulse system

The Agilent Femto Pulse system automated pulsed-field CE instrument is a fast, high-resolution benchtop capillary electrophoresis (CE) platform that utilizes pulsed-field electrophoresis to separate high molecular weight DNA fragments. This platform allows important DNA quality checkpoints to be completed in less than 1.5 hours with minimal sample input for de novo large genome sequencing projects and other PacBio applications leveraging multi-kilobase read lengths. The instrument can be used in place of gel-based pulsed-field electrophoresis (PFGE) systems to fully support generation of large-insert SMRTbell libraries with accurate sizing to 165 kb. Alternative DNA sizing instruments cannot accurately resolve large DNA fragments…

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Wednesday, January 6, 2021

AGBT PacBio Workshop: Full workshop recording

PacBio customers and thought leaders discuss the role SMRT sequencing is playing in comprehensive genomics: past, present, and future. Featuring J. Craig Venter, Gene Myers, Deanna Church, Jeong-Sun Seo and W. Richard McCombie.

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Wednesday, January 6, 2021

Podcast: Marc Salit discusses creating the foundation of genomics

Marc Salit is the leader of the Genome Scale Measurement Group at the National Institute of Standards and Technology or NIST. In this Mendelspod podcast, he explains how NIST played a pivotal, foundational role in enabling the ‘Century of Physics.’ Now Marc and NIST are looking for the right set of standards to enable the already-upon-us “Century of Biology.” The human reference genome is an example of a standard that Marc and his team are developing. Currently they are piloting what they call “Genome in a Bottle,” a physical reference standard to which all other human genomes can be measured.…

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Wednesday, January 6, 2021

Podcast: Frontiers of sequencing – Putting long reads and graph assemblies to work

The Mike Schatz lab at Cold Spring Harbor is well know for de novo genome assemblies and their work on structural variation in cancer genomes. In this Mendelspod podcast, lab leader, Mike Schatz, and doctorate student, Maria Nattestad tell of two new projects that include the de novo assembly of a very difficult but important flatworm genome and, secondly, making better variant calls for oncogenes such as HER2.

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Wednesday, January 6, 2021

Podcast: Reference genome making major strides in ethnic diversity, says Valerie Schneider, NCBI

Valerie Schneider of the National Center for Biotechnology Information discuss how the Genome Reference Consortium (GRC) is bringing more ethnic diversity to the latest human reference assembly (GRCh38) by adding patches and alternate loci scaffolds. Scientists working with population graphs are among the early adopters of these new alternate loci scaffolds. She also discusses work underway at the McDonnell Genome Institute at Washington University to generate a set of high-quality, de novo whole genomes from a wide variety of populations. The new ethnic genomes “are also intended to stand on their own as complements to the reference so users can…

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Wednesday, January 6, 2021

AGBT Virtual Poster: Generation of local reference genomes using PacBio and BioNano data, and analysis of the “dark matter” of structural variants in 1000 Swedish genomes

In this AGBT 2017 poster, Ulf Gyllensten from Uppsala University presents two local reference genomes generated with PacBio and Bionano Genomics data. These assemblies include structural variation and repetitive regions that have been missed with previous short-read efforts, including some new genes not annotated in the human reference genome.

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Wednesday, January 6, 2021

User Group Meeting: The trials and tribulations of high quality human genome assembly

In this PacBio User Group Meeting presentation, Tina Graves-Lindsay of the McDonnell Genome Institute and the Genome Reference Consortium speaks about the importance of phasing human reference genomes. Her team is now working on its fifteenth human genome assembly — part of a major effort to improve genomic representation of ethnic diversity — with a pipeline that generates 60-fold PacBio coverage for a de novo assembly, followed by scaffolding with other technologies. They are also using FALCON-Unzip to separate haplotypes, leading to reference-grade diploid assemblies. This approach has already helped resolve errors seen in other genomes and even the gold-standard…

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Wednesday, January 6, 2021

Webinar: Assembling high-quality human reference genomes for global populations

This webinar highlights global initiatives currently underway to use Single Molecule, Real-Time (SMRT) Sequencing to de novo assemble genomes of individuals representing multiple ethnic populations, thereby extending the diversity of available human reference genomes. In their presentations, Tina Graves-Lindsay from Washington University and Adam Ameur from Uppsala University spoke about diploid assemblies, discovering novel sequence and improving diversity of the current human reference genome. Finally, Paul Peluso of PacBio presented data from the recent effort to sequence a Puerto Rican genome and shared a SMRT Sequencing technology roadmap showing the next several upgrades for the Sequel System.

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Tuesday, December 22, 2020

A low DNA input protocol for high-quality PacBio de novo genome assemblies from single invertebrate individuals

A high-quality reference genome is an essential tool for studies of plant and animal genomics. PacBio Single Molecule, Real-Time (SMRT) Sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. PacBio is the core technology for many large genome initiatives, however, relatively high DNA input requirements (5 µg for standard library protocol) have placed PacBio out of reach for many projects on small, non-inbred organisms that may have lower DNA content. Here we present high-quality de novo genome assemblies from single invertebrate individuals for two different species: the Anopheles…

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Tuesday, December 22, 2020

A low DNA input protocol for high-quality PacBio de novo genome assemblies

A high-quality reference genome is an essential tool for studying the genetics of traits and disease, organismal, comparative and conservation biology, and population genomics. PacBio Single Molecule, Real-Time (SMRT) Sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. Improvements in throughput and concomitant reductions in cost have made PacBio an attractive core technology for many large genome initiatives. However, relatively high DNA input requirements (3 µg for standard library protocol) have placed PacBio out of reach for many projects on small organisms that may have lower DNA content…

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Tuesday, December 22, 2020

Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results

We have streamlined the SMRTbell library generation protocols with improved workflows to deliver seamless end-to-end solutions from sample to analysis. A key improvement is the development of a single-tube reaction strategy that shortened hands-on time needed to generate each SMRTbell library, reduced time-consuming AM Pure purification steps, and minimized sample-handling induced gDNA damage to improve the integrity of long-insert SMRTbell templates for sequencing. The improved protocols support all large-insert genomic libraries, multiplexed microbial genomes, and amplicon sequencing. These advances enable completion of library preparation in less than a day (approximately 4 hours) and opens opportunities for automated library preparation for…

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