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Thursday, November 7, 2019

PAG PacBio Workshop: A-maize-ing time for plant science – SMRT Sequencing of the maize genome and transcriptome

Doreen Ware introduces her team’s new assembly of maize, built with PacBio long-read sequencing and genome maps from BioNano Genomics. With a contig N50 of nearly 10 Mb and more complete information than any previous assembly, Ware says, “This is just an amazing time to be a plant scientist.” Her presentation includes a number of highlights from the new assembly, which may help crop improvement efforts for maize.

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Thursday, November 7, 2019

AGBT Roche and PacBio Workshop: Towards precision medicine

Euan Ashley speaks about precision medicine and said clinical-grade analysis has been limited by complex regions in the human genome. His key theme,”Precision medicine needs to be accurate medicine,” was illustrated with several examples where short-read sequencing or traditional clinical sequencing methods failed to be accurate. Also included: targeted RNA sequencing and gene phasing with long-read sequencing.

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Thursday, November 7, 2019

Podcast: The goal is de novo assembly in the clinic, says Jim Lupski, Baylor

Jim Lupski is a professor at Baylor College of Medicine where he’s on the frontline of incorporating genomic research into everyday clinical practice. The story begins with Jim’s own genome, which is perhaps the most sequenced genome ever. Jim’s life as a leading genomic researcher has been driven in part for a strong personal reason. He has a rare genetic disease named after three researchers who first defined it, Charcot Marie Tooth Neuropathy. What began as a personal journey to uncover the source of his own disease led Jim to seminal work that launched the field of structural variation. Working…

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Thursday, November 7, 2019

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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Thursday, November 7, 2019

PAG Conference: From sequencing to chromosomes – new de novo assembly and scaffolding methods improve the goat reference genome

Sergey Koren of the National Biodefense Analysis and Countermeasures Center (NBACC) discusses integrating the MinHash Alignment Process (MHAP) with Celera Assembler to enable reference-grade assemblies of model organisms, revealing novel heterochromatic sequences and filling low-complexity gap sequences in the GRCh38 human reference genome. Dr. Koren and his team have applied this method to assemble the San Clemente goat genome. Combining SMRT Sequencing and next-generation optical mapping from BioNano Genomics generates an assembly that is over 150-fold more contiguous than the latest Capra hircusgoat reference. In combination with Hi-C sequencing, the assembly surpasses reference assemblies de novo, with minimal manual intervention.…

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Thursday, November 7, 2019

PAG Conference: Approaches taken, progress made, and enhanced utility of long read-based goat, swine, cattle and sheep reference genomes

Tim Smith, molecular geneticist at the USDA Agricutural Research Service (ARS) in Clay Center, Nebraska, and director of the U.S. Meat Animal Reseach Center Core Facilities, discusses the USDA’s efforts to improve the goat, swine, cattle, and sheep genomes through long read-based de novoassemblies scaffolded with a variety of approaches. Recent advances in long-read sequencing, combined with new technologies for scaffolding the resulting contigs, have made it possible to make a significant change in the quality of genome assemblies for a very small fraction of the price required to create the originals. Although a change of reference genomes incurs cost,…

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Thursday, November 7, 2019

AGBT Conference: Long-read sequence of the gorilla genome

Christopher Hill presents data from efforts to produce reference-grade assemblies for the great ape species. Using SMRT Sequencing, Hill and his colleagues are generating assemblies with much higher contiguity to resolve repetitive and other particularly complex regions. In this talk, he focuses on data from their new high-quality gorilla assembly.

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Thursday, November 7, 2019

AGBT Conference: The first African reference genome assembly

Karyn Meltz Steinberg presents the first high quality African reference genome assembly of the Yoruban individual, NA19240, produced from SMRT Sequencing data. She said PacBio sequencing offers significant improvement over short-read sequence data for high-quality assemblies.

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Thursday, November 7, 2019

AGBT Virtual Poster: Unzipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive haplotig assemblies

In this AGBT virtual poster video, Jason Chin, a bioinformatician at PacBio, describes a polyploidy-aware de novo assembly approach called FALCON and a new algorithm, dubbed FALCON-unzip, that involves “unzipping” diploid genomes for de novo haplotype reconstructions from SMRT Sequencing data. These methods are illustrated in a studies of fungal, Arabidopsis and human datasets for the resolution of structural variation and characterization of haplotypes.

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Thursday, November 7, 2019

AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements

In this AGBT poster, PacBio bioinformatician Matthew Seetin presents a new assembly for Aedes aegypti cell line, the mosquito responsible for spreading viruses like Dengue and Zika. SMRT Sequencing generated a gapless assembly with a contig N50 of 1.4 Mb, compared to 82 kb in the previous assembly. The genome features a number of transposable elements and long tandem repeats.

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