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Wednesday, June 26, 2019

Application Updates: Introducing Iso-Seq Express for Faster RNA Sequencing

Seeking to sequence and characterize entire transcriptomes in one go? Our new Iso-Seq protocol and reverse-transcriptase PCR kit makes it easier, speedier and cheaper.  Run on the new Sequel II System, the completely revamped Iso-Seq Express workflow achieves whole transcriptome characterization from a single SMRT Cell 8M delivering up to 400 Gb, and at a third of the cost, or less. Yield has also increased on the Sequel System, with 3.0 sequencing chemistry typically delivering up to 30 Gb per SMRT Cell 1M for our RNA sequencing application.  The new protocol requires three times less RNA input (300 ng) and…

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Thursday, June 20, 2019

At Maryland Genomics, Scientists Deploy Sequel II System for a Wide Range of Applications

Maryland Genomics leaders with the Sequel II System In this blog miniseries, we’re recapping presentations from early access users of the Sequel II System. Today, we summarize Luke Tallon’s report from Maryland Genomics, a PacBio Certified Service Provider. Like the other early access users, Maryland received 32 SMRT Cells for use in evaluating the new sequencing system. They tested them across a range of applications: continuous long-read (CLR) sequencing for humans, plants, insects, and bacteria; and HiFi mode, powered by circular consensus sequencing, for human, microbiome, and other samples. Tallon reports that each SMRT Cell 8M averaged about 92 Gb…

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Monday, June 17, 2019

Broad Institute Scientists Use Sequel II System for Trios, Structural Variant Detection

Kiran Garimella As we geared up for the launch of our new Sequel II System, we had the good fortune of working closely with several expert customers in an early access program. Recently, three of those customers reported on their experience with the new sequencing system in a webinar. In this blog series, we’ll be summarizing each speaker’s presentation, and the full recording is available to view. First up was Kiran Garimella (@KiranGarimella), a senior computational scientist at the Broad Institute who focused on the use of HiFi reads, which are long (>10 kb) and accurate (>99%) sequences produced by…

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Thursday, June 13, 2019

The SMRT Special: Journal Focuses on Advances in SMRT Sequencing

Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…

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Tuesday, June 11, 2019

Genome in a Bottle Consortium Describes Human Genome Structural Variation Benchmark

UPDATE: The paper has been published in Nature Biotechnology A preprint released this week from the Genome in a Bottle (GIAB) Consortium describes a benchmark set of structural variants (SVs), differences ≥50 bp, in the genome of a human male named HG002. The GIAB benchmark is the first to allow measuring precision (false positives) and recall (false negatives) of different approaches to detecting structural variants. The GIAB Consortium also developed a tool, Truvari, to support evaluation of variant call sets against the benchmark. Earlier GIAB benchmarks, first released in 2014 and last updated in 2017, have led to enormous improvements…

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Monday, June 10, 2019

Catching up with Carola and the ‘Solar-Powered’ Sea Slug

Two years ago, Carola Greve and colleagues at the Zoological Research Museum Alexander Koenig in Bonn, Germany, were seeking to #SeqtheSlug as part of the 2017 Plant and Animal SMRT Grant competition, and the popular project was a close runner-up. Greve didn’t give up on her quest to sequence the ‘solar-powered’ sea slug. We caught up with her recently at the SMRT Leiden Scientific Symposium, where her update on the sea slug project earned her a Best Poster award.    Why the sea slug?   Although Mollusca represents the second largest animal phylum with around 85,000 extant species, only 23 mollusc genomes…

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