In this webinar, Ben Auch, Research Scientist, Innovation Lab, University of Minnesota Genomics Center, Cody Sheik, Assistant Professor of Biology, University of Minnesota Duluth, and Harm van Bakel, Assistant Professor of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai provide details of the newly updated microbial whole genome sequencing pipeline, which leverages the multiplexing capabilities of the Sequel System, share new insights into the ecophysiology of Minnesota microbes using long-read sequencing, and show of how whole genome sequencing is used in pathogen surveillance programs at hospitals.
One of the longstanding challenges in infectious disease has been the lack of high-quality reference genomes. However, developments in genome sequencing are helping researchers overcome this barrier. Recently, highly contiguous genome assemblies of Plasmodium falciparum, Aedes aegypti, and multiple trypanosomes have become available. The number of reference genomes for bacteria that cause infectious disease is similarly expanding rapidly. In this webinar Meredith Ashby discusses how these new resources are already yielding new biological insights into critical questions in infectious disease research, including how parasites evade the immune system add how pathogens are adapting to evolutionary pressures.
In this webinar, Jenny Ekholm and Paul Kotturi provide an overview of the PacBio No-Amp targeted sequencing application and its uses for targeting hard-to-amplify genes. This approach couples CRISPR-Cas9 with Single Molecule, Real Time (SMRT) Sequencing to enrich targets, without the need for PCR amplification, and generate complete sequence information with base-level resolution.
Mike Hunkapiller, CEO of Pacific Biosciences, opened the PacBio 2015 ASHG Workshop with a historical perspective of human genome sequencing, starting with the Human Genome Project. While advances have been made in technology, throughput and cost reductions, the quality of genomes hasn’t kept pace with decreases in cost. Hunkapiller shared the news of the company’s launch of the Sequel System – which offers SMRT Sequencing and long reads at seven times greater throughput over the PacBio RS II and roughly half the cost, making it feasible to use the system for de novo assembly of high-quality human genomes. He also…
Rick Wilson, Director of the McDonnell Genome Institute at Washington University in St. Louis titled his talk “Of reference genomes and precious metals” and walked the audience through definitions and standards for the various quality levels for de novo assembled human genomes, e.g., platinum, gold, and silver. He noted that this was a good topic for this session because of the important role PacBio has played in the community’s work to create reference-grade genomes. For example, PacBio technology has enabled them to sequence additional genomes (CHM1, CHM13) to a very high quality level. Although these sequences were essential for further…
Richard Gibbs, Director of Baylor College of Medicine’s Human Genome Sequencing Center, talked about the transition to genomic medicine. This hasn’t been as simple as people would like due to such issues as the incomplete reference genome, the difficulty in characterizing some variation, and the lack of knowledge about the function of some genes. At Baylor, most of the human genome sequencing is done for children with Mendelian disorders. He said that among 7,000 samples processed using short-read exome sequencing, only about 25% of these cases are solved. The relatively low diagnosis rate is likely due to structural variation and…
Jonas Korlach, Chief Scientific Officer at PacBio, discussed the technology waves that have followed the initial human genome sequencing project, where we are today, and where we are going. Today, we are in what Korlach calls the 4th wave, where more comprehensive whole-genome re-sequencing is occurring, and we are nearing the 5th, when we will actually be able to free ourselves from reference genomes and sequence everything de novo.
In this webinar, Elizabeth Tseng from PacBio demonstrates how to run the Iso-Seq bioinformatics software pipeline that is part of PacBio’s SMRTAnalysis software suite. Both the web portal interface (SMRT Portal) and the command line version will be introduced. In addition, she reviews the community version of Iso-Seq (pbtranscript-tofu) and other community tools to perform additional analyses.
In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.
Brett Hannigan, Computational Biology Project Leader at DNAnexus, demonstrates a fast, accurate, and cost-efficient solution for diploid-aware de novo genome assembly utilizing FALCON on the DNAnexus platform.
Dr. Olga Vinnere Pettersson, Uppsala Genome Center (Uppsala University), presents best practices for qualifying genomic DNA from a variety of sources to be suitable for Single Molecule, Real-Time Sequencing. Factors that affect single molecule sequencing and recommendations for extracting high-quality genomic DNA will be described. (requires file download to view)
PacBio scientists Kristi Kim and Michael Weiand present on high-throughput solutions for sample preparation including 10 kb template preparation, high-throughput PacBio RS II sample prep kits, and compatible automated liquid handling platforms.
This seminar features great hands-on information and best practices for analyzing SMRT Sequencing data for eukaryotic genome assembly. Michael Schatz provides an overview of the assembly tools, provides recommendations for when to use each one, and discusses the challenges of short-read assemblies. James Gurtowski gives an in-depth overview of hybrid assemblies methods, where short read data are used used to correct errors in longer reads. Finally, Sergey Koren presents on chromosome-scale assembly, including the MinHash Alignment Process (MHAP) he developed to dramatically reduce the computational processing power required for genome assemblies.
In this webinar, Emily Hatas of PacBio shares information about the applications and benefits of SMRT Sequencing in plant and animal biology, agriculture, and industrial research fields. This session contains an overview of several applications: whole-genome sequencing for de novo assembly; transcript isoform sequencing (Iso-Seq) method for genome annotation; targeted sequencing solutions; and metagenomics and microbial interactions. High-level workflows and best practices are discussed for key applications.
The Iso-Seq method enables the sequencing of transcript isoforms from the 5’ end to their poly-A tails, eliminating the need for transcript reconstruction and inference. This webinar provides a comprehensive guide to Iso-Seq method data analysis, bioinformatics, and review key applications.