Are You Working on Coronavirus?
Explore our COVID-19 sequencing tools and resources
Sequence the microbial world with confidence
Microbes account for most of the diversity of life on our planet, yet fewer than 1% have been identified. To understand this ever-evolving world, scientists need the unbiased, accurate, and comprehensive information that only PacBio long-read sequencing can provide.
See the details that drive biological insights with highly accurate, closed genomes that include epigenetic information.
Prokaryotic methylation | Why closed genomes?
Address global needs for novel therapeutics, environmental remediation, and efficient chemical production by mining even the most difficult to sequence microbial genomes.
Biofuel research at JGI | Natural product discovery | Scalable biosynthesis
Advance human health worldwide with new insights into the viruses, bacteria, and protozoa that cause infectious disease.
HIV | Cholera | Malaria | Sleeping sickness | Chagas | Leishmania
Protect public health by finding all the variant types that drive the spread of antimicrobial resistance and contribute to bacterial virulence.
Klebsiella in hospitals | MRSA surveillance | Food safety | Tuberculosis virulence
Explore the role of microbial symbionts and pathogens in plant and animal health and disease.
Entomopathogen biology | Closed Xanthomonas genomes | Methylation directs a pathogen lifecycle
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Whole Genome Sequencing Assemble microbial genomes that are the gold standard for both completeness and accuracy with ease and confidence |
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Metagenomics Comprehensively characterize metagenomes with long, highly accurate, single-molecule reads – no assembly required |
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Bacterial Epigenetics Detect the recognition motifs of active R-M systems at coverage levels recommended for assembly |
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Viral Populations Use long, highly accurate single-molecule reads to deconvolute complex populations, track viral evolution and quantify minor variants |
Selected Resources
- Grech-Baran, Marta et al. (2020) Extreme resistance to Potato virus Y in potato carrying the Rysto gene is mediated by a TIR-NLR immune receptor. Plant biotechnology journal
- Loit, Kaire et al. (2019) Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Applied and environmental microbiology
- Callahan, Benjamin J et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research
- Tørresen, Ole K et al. (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic acids research
- Bickhart, Derek M et al. (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology
- Jensen, Torbjørn Ølshøj et al. (2019) Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nature communications
- Martijn, Joran et al. (2019) Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environmental microbiology
- Forde, Brian M et al. (2019) SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Scientific reports
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Davies, Mark R et al. (2019) Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nature genetics
- Nye, Taylor M et al. (2019) DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PLoS pathogens
- Breitwieser, Florian P et al. (2019) Human contamination in bacterial genomes has created thousands of spurious proteins. Genome research
- Woodson, Evonne et al. (2019) Reduced frequency of HIV superinfection in a high-risk cohort in Zambia. Virology
- Johnston, Christopher D et al. (2019) Systematic evasion of the restriction-modification barrier in bacteria. Proceedings of the National Academy of Sciences of the United States of America
- Stinson, Lisa F et al. (2019) The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Frontiers in microbiology
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- Su, Bin et al. (2019) Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. The Journal of antimicrobial chemotherapy
- Jamy, Mahwash et al. (2019) Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity BioRxiv
- Lui, Wing-Yu et al. (2019) SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection. Emerging microbes & infections
- Ashton, P M et al. (2019) Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans. Nature communications
- Jayaraman, Siddharth et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS neglected tropical diseases
- Murphy, Timothy F et al. (2019) Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. The Journal of infectious diseases
- Fischer, Sebastian et al. (2019) A unique methylation pattern by a type I HsdM methyltransferase prepares for DpnI rare cutting sites in the Pseudomonas aeruginosa PAO1 genome. FEMS microbiology letters
- Sierra, Johanna C et al. (2019) a-Difluoromethylornithine reduces gastric carcinogenesis by causing mutations in Helicobacter pylori cagY. Proceedings of the National Academy of Sciences of the United States of America
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Olarte, Rodrigo A et al. (2019) Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum. BMC genomics
- Pinzone, Marilia Rita et al. (2019) Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nature communications
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Mehta, Devang et al. (2019) A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic acids research
- Sullivan, Mitchell J et al. (2019) Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events BioRxiv
- Biessy, Adrien et al. (2019) Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental microbiology
- Hiraoka, Satoshi et al. (2019) Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature communications
- Nilsson, R Henrik et al. (2019) Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature reviews. Microbiology
- Liang, Quanhui et al. (2019) Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Frontiers in microbiology
- Poster: Portik, Daniel et al. (2020) Metagenomic analysis of type II diabetes gut microbiota using PacBio HiFi reads reveals taxonomic and functional differences
- Poster: Sovic, Ivan et al. (2020) Improving long-read assembly of microbial genomes and plasmids
- Poster: Ashby, Meredith et al. (2020) Low-input single molecule HiFi sequencing for metagenomic samples
- Poster: Holm, Johanna B. et al. (2020) Comparative metagenome-assembled genome analysis of “Candidatus Lachnocurva vaginae”, formerly known as Bacterial Vaginosis Associated bacterium – 1 (BVAB1)
- Poster: Baybayan, Primo et al. (2020) New advances in SMRT Sequencing facilitate multiplexing for de novo and structural variant studies
- Poster: Ashby, Meredith et al. (2020) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Ashby, Meredith et al. (2019) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Jain, S. et al. (2019) Comparison of sequencing approaches applied to complex soil metagenomes to resolve proteins of interest
- Poster: McComb, E. et al. (2019) High-resolution evaluation of gut microbiota associated with intestinal maturation in early preterm neonates
- Poster: Hong, Bo-young et al. (2019) Microbiome profiling at the strain level using rRNA amplicons
- Poster: Ekholm, Jenny et al. (2019) Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results
- Poster: Wong, J. et al. (2018) Single chromosomal genome assemblies on the Sequel System with Circulomics high molecular weight DNA extraction for microbes
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Hall, Richard et al. (2017) Using the PacBio Sequel System to taxonomically and functionally classify metagenomic samples in a trial of patients undergoing fecal microbiota transplantation
- Poster: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Poster: Heiner, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- Blethrow, Justin and Smith, Melissa L. and Vinnere Pettersson, Olga (2021) Webinar: Unleashing the Power of HiFi Sequencing – How the Sequel IIe System Removes Barriers and Empowers Life Scientists
- Miller, Dave and Hernandez, Alvaro (2021) Creating Core Demand with HiFi Sequencing
- Korlach, Jonas (2021) PacBio Sequencing for SARS-CoV-2 Surveillance
- Wenger, Aaron (2021) Not All Long Reads Are Equal – High Accuracy Sets PacBio Apart
- Miller, David and Smith, Melissa Laird (2021) The Long and Short of Sequencing – Why HiFi Reads are the Future
- Becker, Aaron and Ekholm, Jenny and Harris, Charlotte and Kingham, Brewster and Vinnere Pettersson, Olga (2021) SMRT Sequencing as a Service – How to Bring Long-Read Technology to Your Core Lab
- Korlach, Jonas (2021) AGBT Presentation: Increasing the Solve Rate of Rare and Undiagnosed Genetic Diseases with HiFi Sequencing
- Ashby, Meredith and Gehrig, Jeanette (2021) Webinar: Long Reads Versus More Reads Comparing Two Sequencing Tools for Evaluating Live Biotherapeutics as
- Sovic, Ivan and Kronenberg, Zev and Dunn, Christopher and Drake, James and Wong, Joan and Weber, Kristina L. and Browne, Dan and Ashby, Meredith (2020) Video Poster: Improving long-read assembly of microbial genomes and plasmids
- Levandoski, Michael (2020) Webinar: Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States
- (2020) Application Tutorial: Introduction to Variant Detection with HiFi Reads
- (2020) Introduction to highly accurate long-read sequencing (HiFi Sequencing)
- Holm, Johanna (2020) Virtual Global Summit: Shining Light On An Elusive Bug – A comparative metagenome-assembled genome analysis of “Candidatus Lachnocurva vaginae”, formerly known as Bacterial Vaginosis Associated Bacterium – 1 (BVAB1)
- Ashby, Meredith (2020) Virtual Global Summit: The HiFi sequencing advantage for metagenome assembly
- Hernandez, Alvaro (2020) Virtual Global Summit: Using the unique capabilities of the Sequel II System for de novo genome assembly and full-length 16S sequencing
- Tseng, Elizabeth and Wilson, Joan and Hon, Ting and Eng, Kevin and Lambert, Christine and Chakraborty, Shreyasee and Zhu, Lei and Toepfer, Armin and Xiang, Wenwen and Harting, John and Li, Qiang and Underwood, Jason G. and Baybayan, Primo and Ashby, Meredith and Bostick, Maggie and Farmer, Andrew (2020) Video Poster: Long-read sequencing of the SARS-CoV-2 genome and the human immune repertoire
- (2020) Video: HiFi Sequencing – Unlock your next great discovery
- Ashby, Meredith and Portik, Daniel and Weber, Kay (2020) Webinar: Bioinformatics lunch & learn – A quick guide to metagenomic analysis with PacBio HiFi reads
- Guarco, Carmen and Hernandez, Álvaro G. (2020) Spanish Language Webinar: Introducción a la secuenciación larga y precisa con PacBio
- Wenger, Aaron (2020) Educational Video: Variant Detection with HiFi Reads – Understanding Results from the precisionFDA Truth Challenge
- Oliveira, Pedro (2020) SMRT Leiden: Epigenomics in the ERA of third-generation sequencing: A large-scale study of the human pathogen Clostridioides difficile
- Ashby, Meredith and Laird-Smith, Melissa and Watson, Corey (2020) Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research
- Ashby, Meredith and Ma, Bing and Weinstock, George (2020) Webinar: A HiFi View – Sequencing the gut microbiome with highly accurate long reads
- Weber, Kay (2020) Webinar: Bioinformatics lunch & learn – HiFi assembly
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Browne, Dan (2019) Webinar: Bioinformatics lunch & learn – Better assemblies of bacterial genomes and plasmids with the new microbial assembly pipeline in SMRT Link v8.0
- Ashby, Meredith and Eversole, Kelley (2019) Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing
- Wheeler, Nic (2019) User Group Meeting: Long-read RNA Sequencing in neglected human parasites
- Nakanishi, Masako (2019) User Group Meeting: Modulation of gut microbiome in mice with differential susceptibility to colonic ulceration
- Polson, Shawn (2019) User Group Meeting: New genotype to phenotype associations in viral metagenomes enabled by SMRT Sequencing
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2021)
- Application Brochure: What can you do with one SMRT Cell? (2021)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2020)
- Product Brochure: Sequel IIe System – Sequencing evolved (2020)
- Informational Guide: Understanding accuracy in DNA sequencing (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Technical Note: Preparing DNA for PacBio HiFi sequencing – Extraction and quality control (2020)
- Informational Guide: Looking beyond the single reference genome to a pangenome for every species (2020)
- Application Brief: Microbial whole genome sequencing – Best Practices (2020)
- PacBio Certified Service Providers (2020)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- Infographic: A brief history of microbiology (2019)
- Case Study: Mining complex metagenomes for protein discovery with long-read sequencing (2019)
- Application Note: Microbial multiplexing workflow on the Sequel System (2019)