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Thursday, January 7, 2021

Whitepaper: Structural variation in the human genome

Structural variation accounts for much of the variation among human genomes. Structural variants of all types are known to cause Mendelian disease and contribute to complex disease. Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution and genetic diversity.

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Thursday, January 7, 2021

Case Study: Mining complex metagenomes for protein discovery with long-read sequencing

The bacteria living on and within us can impact health, disease, and even our behavior, but there is still much to learn about the breadth of their effects. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and the public alike. Scientists at Second Genome are hoping to apply these insights to improve human health, leveraging their bioinformatics expertise to mine bacterial communities for potential therapeutics. Recently they teamed up with scientists at PacBio to explore how long-read sequencing might supplement their short-read-based pipeline for gene discovery, using an environmental sample as a test…

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Thursday, January 7, 2021

Application Brief: Long-read RNA sequencing – Best Practices

With Single Molecule, Real-Time (SMRT) Sequencing and the Sequel Systems, you can easily and affordably sequence complete transcript isoforms in genes of interest or across the entire transcriptome. The Iso-Seq method allows users to generate full-length cDNA sequences up to 10 kb in length — with no assembly required — to confidently characterize full-length transcript isoforms.

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Thursday, January 7, 2021

Informational Guide: What’s the value of sequencing full-length RNA transcripts?

The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing using a full-length transcript approach become clearer.

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Wednesday, January 6, 2021

AGBT 2015 Highlights: Customer interviews day 1

PacBio customers discuss their applications of PacBio SMRT Sequencing and long reads, including Lemuel Racacho (Children’s Hospital of Eastern Ontario Research Institute), Matthew Blow (JGI), Yuta Suzuki (U. of Tokyo), Daniel Geraghty (Fred Hutchinson Cancer Center), and Mike Schatz (CSHL)

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Wednesday, January 6, 2021

Podcast: Going beyond the $1,000 genome with Mark Gerstein

Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project. “I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of this Mendelspod interview. “The great excitement of next generation sequencing—which is deserved—has…

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Wednesday, January 6, 2021

PAG Conference: Update on sequencing of the Cabernet sauvignon genome

Grant Cramer from the University of Nevada, Reno, and Dario Cantu from the Univeristy of Callifornia, Davis, discuss past challenges with sequencing Clone 8 of Cabernet Sauvignon (Vitis vinifera). An assembly of the genome was attempted with approximately 110x Illumina reads and 5x PacBio reads. The PacBio SMRT Sequencing read made major improvements in the assembly compared with the results of Illumina reads only. However, the assembly results were still unsatisfactory, so an additional 100-fold SMRT Sequencing coverage had been generated. An update on the current sequencing results and status of the assembly are presented.

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Wednesday, January 6, 2021

Video: Using the Integrative Genomics Viewer (IGV) to visualize PacBio long-read SMRT Sequencing data

In this video, PacBio scientists present ongoing improvements to the Integrative Genomics Viewer (IGV) and demonstrate how multiple new features improve visualization support for PacBio long-read sequencing data. The video describes these recent updates which include; quick consensus accuracy mode to hide random single-molecule errors, direct phasing of haplotypes using long-read evidence, and visual annotation of insertions and deletions relative to the reference with enumeration of gap size for individual reads. These new features are available now in the development version of IGV, which can be found at http://software.broadinstitute.org/software/igv/download_snapshot. The Sequel sequencing data used in this demonstration is also publicly…

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Wednesday, January 6, 2021

i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing

PacBio Sequencing is characterized by very long sequence reads (averaging > 10,000 bases), lack of GC-bias, and high consensus accuracy. These features have allowed the method to provide a new gold standard in de novo genome assemblies, producing highly contiguous (contig N50 > 1 Mb) and accurate (> QV 50) genome assemblies. We will briefly describe the technology and then highlight the full workflow, from sample preparation through sequencing to data analysis, on examples of insect genome assemblies, and illustrate the difference these high-quality genomes represent with regard to biological insights, compared to fragmented draft assemblies generated by short-read sequencing.

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