In this PacBio User Group Meeting presentation, Garth Ehrlich of Drexel University College of Medicine shares his work on developing a microbiome assay that uses SMRT Sequencing to provide high-quality coverage of the 16S bacterial rRNA for species identification. The microbiome analysis pipeline, MCSMRT, takes advantage of PacBio circular consensus sequencing (CCS) technology and second-generation pathway analysis system for generating extremely high-fidelity sequences that provide the user with ultra-high-confidence species-level microbiome data.
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 PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. By using SMRT Sequencing, his team generated higher-resolution data about viral genomes and aims to use this information as a guide to how these genomes function.
In this PacBio User Group Meeting lightning talk, Masako Nakanishi presents a study of how the gut microbiome alters an organism’s susceptibility to colonic ulceration; next, she plans to examine cause and effect by evaluating results of fecal transplants in mice.
In this PacBio User Group Meeting presentation, PacBio scientist Meredith Ashby shared several examples of analysis — from full-length 16S sequencing to shotgun sequencing — showing how SMRT Sequencing enables accurate representation for metagenomics and microbiome characterization, in some cases even without fully assembling genomes. New updates will provide users with a dedicated microbial assembly pipeline, optimized for all classes of bacteria, as well as increased multiplexing on the Sequel II System, now with 48 validated barcoded adapters. That throughput could reduce the cost of microbial analysis substantially.
In this Labroots webinar, Meredith Ashby, Director of Microbial Genomics at PacBio, describes the utility of highly accurate long-read sequencing, known as HiFi sequencing, to understand the SARs-CoV-2 viral genome. HiFi sequencing enables mutation phasing and rare variant detection to understand viral stability and mutation rates, as well as providing insights into viral population structure for monitoring viral evolution. Ashby also shares how HiFi sequencing can be used to explore the host immune response to COVID-19, specifically by providing full-length sequencing of the B cell repertoire, IGH locus and HLA genes. Access additional COVID-19 Sequencing Tools and Resources.
Studying microbial genomics and infectious disease? Learn how the PacBio Sequel II System can help advance your research, with first-hand perspectives from scientists who are investigating SARS-CoV-2 and COVID-19. In this webinar, Melissa Laird-Smith (Mt. Sinai School of Medicine) discusses her work evaluating the impact of host immune restriction in health and disease with high resolution HLA typing. She is joined by Corey Watson (University of Louisville School of Medicine) who talks about overcoming complexity to elucidate the role of IGH haplotype diversity in antibody-mediated immunity. Hosted by Meredith Ashby, Director of Microbial Genomics at PacBio. Access additional PacBio resources…
Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…
Jana U’Ren of the University of Arizona discusses the fungi that live inside of plants at a PacBio workshop at the PAG 2020 conference. U’Ren studies the biology and evolution of mycorrhizal fungi found in the photosynthetic tissue of plant leaves, which are grouped together functionally as endophytes. In this video, she shares some of her preliminary findings collecting and analyzing samples from Boreal forests around the world.
In this webinar, Dr. Ashby gives attendees a brief update on PacBio’s metagenomics solutions on the Sequel II System. Then, Dr. Ma, University of Maryland School of Medicine, discusses her work using long read sequencing to identify high-resolution microbial biomarkers associated with leaky gut syndrome in premature infants. Finally, Dr. Weinstock, The Jackson Laboratory, talks about the potential of highly accurate long reads to enable strain-level resolution of the human gut microbiome by resolving intraspecies variation in multiple copies of the 16S gene.
COVID-19 is caused by the infection of SARS-CoV-2, a member of the coronavirus family. Complete and accurate sequencing of the SARS-CoV-2 genome enables discovery and epidemiological tracing of mutations that may be important for antiviral and vaccine research. A complementary approach, sequencing the patients’ immune repertoire, allows for detection of neutralizing antibodies and understanding variation in the adaptive immune response. PacBio’s SMRT Sequencing uses circular consensus sequencing that can generate long, highly accurate (HiFi) reads. We find that a tiled multiplex PCR amplicon approach of ~1-2 kb fragments achieves a balanced tradeoff between ease of library preparation and robustness to…
In this webinar, Jonas Korlach, Chief Scientific Officer, PacBio provides an overview of the features and the advantages of the new Sequel II System. Kiran Garimella, Senior Computational Scientist, Broad Institute of MIT and Harvard University, describes his work sequencing humans with HiFi reads enabling discovery of structural variants undetectable in short reads. Luke Tallon, Scientific Director, Genomics Resource Center, Institute for Genome Sciences, University of Maryland School of Medicine, covers the GRC’s work on bacterial multiplexing, 16S microbiome profiling, and shotgun metagenomics. Finally, Shane McCarthy, Senior Research Associate, University of Cambridge, focuses on the scaling and affordability of high-quality…
To start Day 1 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on the latest releases and performance metrics for the Sequel II System. The longest reads generated on this system with the SMRT Cell 8M now go beyond 175,000 bases, while maintaining extremely high accuracy. HiFi mode, for example, uses circular consensus sequencing to achieve accuracy of Q40 or even Q50.
In this short video, Aaron Wenger, a Principal Scientist at PacBio, explains what highly accurate long reads, or HiFi reads, are and how they help to detect all variant types including single nucleotide, indels, and structural variants. He goes on to recap the precisionFDA Truth Challenge V2 which used Genome in a Bottle (GIAB) benchmarks to evaluate various sequencing technologies. In the 2020 challenge, when ranked for accuracy, PacBio HiFi reads delivered the highest precision and recall in all categories.