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Thursday, August 31, 2017

Sequel System Data Release: Iso-Seq Results for Hummingbird and Zebra Finch Brain Tissue

Anna’s hummingbird photo by Pat Durkin If you’re interested in avian vocal learning or want to explore a PacBio Iso-Seq data set generated with the Sequel System, we have good news. We’ve just released data from Iso-Seq interrogations of brain tissue from two avian models of vocal learning, Anna’s hummingbird (Calypte anna) and zebra finch (Taeniopygia guttata), sequenced in collaboration with the Erich Jarvis and Olivier Fedrigo labs at the Rockefeller University. If you’re not familiar with the Iso-Seq method, it’s the long-read sequencing answer to short-read RNA-seq studies. By using SMRT Sequencing for a transcriptome project, scientists can generate…

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Monday, August 28, 2017

With Iso-Seq Study, Scientists Reveal Complexity of Rabbit Transcriptome

Photo by Paulo Costa A new paper in Scientific Reports presents results from a transcriptome analysis for Oryctolagus cuniculus. The work was done with SMRT Sequencing, which allowed scientists to discover novel transcripts and increase the diversity of known transcripts for the rabbit. “A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing” comes from lead authors Shi-Yi Chen and Feilong Deng, senior author Song-Jia Lai, and collaborators at Sichuan Agricultural University. In the paper, the scientists note that an ongoing challenge in rabbit studies has been the dearth of gene-level data. “Most of the existing gene models are…

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Thursday, August 24, 2017

Software Tools Optimized for Long Reads Improve Detection of Complex Structural Variants

[Update April 30, 2018: This paper is now published in Nature Methods.] Sniffles and NGMLR, structural variant detection and alignment algorithms developed in the Schatz lab for long-read sequence data, are already familiar to many in the PacBio community. Now, a preprint is available so users can see how these open-source tools perform in a variety of conditions. “Accurate detection of complex structural variations using single molecule sequencing” comes from lead author Fritz Sedlazeck at Baylor College of Medicine, senior author Michael Schatz at Johns Hopkins University, and collaborators. The team notes that long-read sequencing has introduced a much more…

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Tuesday, August 15, 2017

In Bake-Off, SMRT Sequencing Generates Highest-Quality, Cost-Effective Bacterial Assembly

From CDC/Courtesy of Larry Stauffer, Oregon State Public Health Laboratory Scientists from the University of Hong Kong recently reported results of a head-to-head comparison of long-read and short-read platforms for sequencing and assembly of a bacterial genome. They determined that only SMRT Sequencing was capable of generating highly accurate, complete assemblies. “Completing bacterial genomes should no longer be regarded as a luxury, but rather as a cost-effective necessity,” the team reports. “PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome” was published in Frontiers in Microbiology by lead author Jade…

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Wednesday, August 9, 2017

Iso-Seq Analysis Reveals Differential Expression in Male and Female Abalones

Photo by Toby Hudson Earlier this year, scientists from Korea reported results from a transcriptome study of Pacific abalone. In this paper, the team used SMRT Sequencing to demonstrate that alternative splicing and gene expression have sex-specific signatures in these organisms. “Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai” comes from lead authors Mi Ae Kim and Jae-Sung Rhee, senior author Young Chang Sohn, and collaborators. They focused on abalone, a marine gastropod, because of its importance to Korean aquaculture: the species they studied is estimated to represent about 10,000 metric tons of…

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Monday, August 7, 2017

SMRT Sequencing Shines at ISAG: First Sequel System Bovine Genome Presented

If you weren’t at the 36th International Society for Animal Genetics Conference in Dublin, you missed more than a chance to drink Guinness and practice an Irish brogue. The PacBio team had a great time at ISAG, learning about the latest in animal science and updating attendees on the advantages of SMRT Sequencing for generating high-quality genome assemblies and annotations. The conference drew more than 750 scientists from around the world, and we were truly impressed by the quality of research they presented in talks and posters. Long-read PacBio sequencing is already making a difference for scientists in this community,…

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Thursday, August 3, 2017

At Baltimore UGM, New Tools and Research Breakthroughs with SMRT Sequencing

We were delighted to be back at the University of Maryland this summer for our annual East Coast User Group Meeting. The day-long event, preceded by half-day workshops on sample prep and bioinformatics, exceeded our expectations. From the packed session hall to the terrific science and great discussions, the UGM facilitated the exchange of best practices and new suggestions for optimizing SMRT Sequencing performance for a variety of applications. Below is a recap of the day’s highlights, with several of the presentations available to download. PacBio scientist Aaron Wenger presented the Structural Variant Calling application that is included in the…

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Tuesday, August 1, 2017

To Resolve KIR Region, Scientists Pair SMRT Sequencing with Fosmid Cloning

A paper from scientists at the National Marrow Donor Program, Center for International Blood and Marrow Transplant Research, Fred Hutchinson Cancer Research Center, and other institutions reports the use of SMRT Sequencing to characterize the challenging killer cell immunoglobulin-like receptor (KIR) region in eight human genomes. By sequencing full-length fosmids, they found previously unreported haplotype structures. “Revealing Complete Complex KIR Haplotypes Phased By Long-Read Sequencing Technology” comes from lead author David Roe, senior author Martin Maiers, and collaborators. They targeted the KIR region — which has implications in autoimmune disease, transplantation, infections, and more — because it has historically been…

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