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Sunday, October 25, 2020

PAG PacBio Workshop: Using PacBio reads and pbjelly software to improve genomes – a cost-effective approach to finishing

Kim Worley from Baylor’s Human Genome Sequencing Center describes the improvement of the sooty mangabey primate genome. Sooty mangabey is a model organism for HIV research, since this particular primate can be infected with the immunodeficiency virus and never develop any symptoms. Worley and her team used PacBio long reads in conjunction with their own assembly tool, PBJelly, closing 64% and improving another 19% of the gaps.

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Sunday, October 25, 2020

PAG PacBio Workshop: Sequencing the Potentilla micrantha genome to study the evolution of fruiting in strawberry

Judson Ward, principal scientists at Driscoll’s Strawberries in California, introduces a genome assembly for Potentilla micrantha, which is closely related to strawberry but lacks fleshy ‘fruits’ or berries. Comparative genomics between P. micrantha and strawberry will yield significant information regarding the genetic mechanisms controlling fruit development. Using SMRT Sequencing Driscoll’s sequenced the 240 Mb P. micaranthagenome and produced a draft genome assembly, spanning the majority of the predicted sequence length. A comparison of sequence data produced using the Illumina HiSeq2000 and the PacBio RS platform demonstrated that PacBio sequencing produced a significantly longer N50 contig size and permitted a more complete genome…

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Sunday, October 25, 2020

AGBT Conference: Whole human genome SMRT Sequencing reveals uncharacterized structural variations providing a path to more informed diagnostic testing

In this AGBT talk, Mount Sinai’s Eric Schadt uses PacBio sequencing on human genomes and reports finding uncharacterized structural variation that could have diagnostic utility. Schadt says that SMRT sequencing is advantageous for long-range genetic information, extreme GC content, and highly repetitive regions. He presents sequence data for a CEPH individual studied for repeat expansions, showing that long reads can resolve the majority of these regions.

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Sunday, October 25, 2020

AGBT Conference: Automated de novo genome assemblies and bacterial epigenomes using PacBio sequencing

In this AGBT plenary talk, Jonas Korlach presented a number of collaborative studies between PacBio and other institutions to make use of highly accurate, long-read sequence data, which has led to a revival of finished genomes. Examples from the infectious disease or pathogen realm included Pertussis, Salmonella, and Listeria, all of which now have closed genomes from PacBio-generated data. Korlach also reported on epigenomic information in Salmonella and Listeria, indicating potential new forms of DNA modifications.

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Sunday, October 25, 2020

ASM PacBio Workshop: Genomics in food security – 100k pathogen genome project

UC Davis’s Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology.

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Sunday, October 25, 2020

Customer Experience: PacBio at Sanger Institute – de novo assembly, methylation analysis, and detection of rare variants

Harold Swerdlow, who formerly ran the R&D department at Wellcome Trust Sanger Institute, discusses the Sanger team’s use of the PacBio RS sequencer. He says the system is uniquely suited for de novo sequencing and genome assembly, methylation pattern identification, and low-level variant detection because of its long reads and high-accuracy, single-molecule sequencing. At Sanger, that makes a real difference for the large-scale projects they have in cancer biology, pathogen sequencing, and human genetics.

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Sunday, October 25, 2020

Customer Experience: Sequencing through GC-rich microbial genomes with the high-accuracy PacBio RS

The Genome Analysis Centre’s (TGAC) Matthew Clark, who leads the sequencing technology development group, says that high-accuracy PacBio sequencing is ideal for GC-rich or AT-rich genomes since it shows no GC bias. This has enabled his team to sequence several strains of Streptomyces and elucidate gene clusters thought to be important in antibiotic production. Clark says long reads from SMRT Sequencing are good for other hard-to-sequence regions, such as repeats or large transposable elements.

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Sunday, October 25, 2020

AGBT Conference: Automated, non-hybrid de novo genome assemblies and epigenomes of bacterial pathogens

Jonas Korlach, CSO of PacBio, discusses the revival of finished genomes the microbial community will see with long read data, emphasizing that for certain organisms such as rapidly evolving microbes, having a de novo finished genome will be more useful than creating a draft based on a previous related reference genome. Korlach describes two bioinformatic methods from PacBio, a hierarchical genome assembly process (HGAP) and an consensus caller (Quiver), which are used to generate finished genomes from just long-read PacBio data, with final genome sequence accuracies over 99.999%. Korlach demonstrates the ability of PacBio data to generate closed, high-quality de…

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