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Wednesday, December 11, 2019

Long-Read Sequencing Could Improve the Sensitivity and Precision of 16S Studies Says Jackson Lab Study

It’s time to revisit the way scientists are using 16S rRNA gene sequencing to study microorganisms, according to a team of Jackson Laboratory researchers.  Popular targets for taxonomy and phylogeny studies because of their highly conserved nature, amplified sequences of the 16S ribosomal RNA genes can be compared with reference databases to determine the identity of the microorganisms that comprise a metagenomic sample. Sequences with a > 95% match are generally considered to represent the same genus, for example, while > 97% matches are considered the same species. However, these matches are often made by sequencing only part of the nine-region, ~1500 bp…

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Tuesday, March 12, 2019

AGBT 2019: First Look at Early Access Results from the Sequel II System

The PacBio team was honored to have the opportunity to give several talks at this year’s Advances in Genome Biology & Technology conference. If you weren’t able to be there, we’ve got you covered with videos and highlights. In a plenary session, Marty Badgett, senior director of product management, gave attendees a look at the latest results using the HiFi reads with the circular consensus sequencing (CCS) mode as well as a sneak peek at data from our soon-to-be-released Sequel II System. As he demonstrated, HiFi reads cover the same molecule many times, delivering high consensus accuracy (Q30 or 99.9%)…

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Wednesday, March 6, 2019

GIAB Expands Variant Call Sets with SMRT Sequencing Results

Genome in a Bottle Consortium You may have missed last week’s Advances in Genome Biology & Technology conference in sunny Marco Island, Fla., but you definitely shouldn’t miss the two posters presented there by Justin Zook and Justin Wagner from NIST’s Genome in a Bottle (GIAB) consortium. The GIAB team has made critical progress in generating high-quality human genome reference materials and benchmarks that have helped to improve the accuracy and reproducibility of variant calling across laboratories. The latest results advance that work with an expansion of the benchmark set to include additional small (single-nucleotide variant and indel) variants and…

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Wednesday, January 16, 2019

Q&A: Scientists Discovered Somatic Recombination in the Brain. Now What?

Jerold Chun The recent Nature paper describing the first evidence of somatic gene recombination in the human brain has been getting so much attention that we went back to the lab’s PI to learn more. Jerold Chun is Professor in the Degenerative Diseases Program and Senior Vice President of Neuroscience Drug Discovery at Sanford Burnham Prebys Medical Discovery Institute in La Jolla, Calif. He spoke with us about this remarkable discovery in the APP gene in patients with sporadic Alzheimer’s disease, the decades-long hunt for somatic recombination in genes active in the brain, and how SMRT Sequencing made a difference.…

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Tuesday, January 15, 2019

One For All: HiFi Long Reads for de Novo Assembly and Comprehensive Variant Detection

UPDATED August 12, 2019 This paper is now published in Nature Biotechnology. ORIGINAL POST January 15, 2019 CCS read protocol We’re excited to report on new SMRT Sequencing advances that will ultimately help users generate extremely accurate, single-source data for large-scale genome projects. We demonstrate this new approach in a preprint on bioRxiv, and intend to fully support the new data type in upcoming product releases for the broader SMRT Sequencing community. The preprint describes a collaborative effort to comprehensively characterize a human genome — we chose the well-analyzed HG002/NA24385 sample available as a benchmark from the Genome in a…

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