Microbial whole genome sequencing

Generate closed chromosomes and plasmids from even the most repeat-dense and GC-rich genomes, easily, affordably, and at high-throughput.

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Complete microbial genomes with ease and confidence

For most microbes, closed genomes with accessory plasmids can be assembled with one touch using the default settings of our assembly pipeline.

  • Generate platinum-standard, closed reference genomes
  • Identify ever-evolving genes associated with toxicity, virulence, and antimicrobial resistance
  • Resolve strains, serotypes, and plasmids to track pathogen outbreaks in humans, plants, and animals, through food systems, hospitals, and communities
  • Comprehensively characterize microbes to facilitate scientific breakthroughs

Workflow: From DNA to characterized microbial genomes in a single experiment

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Library preparation

Starting with unamplified genomic DNA, prepare libraries for whole genome sequencing using standardized protocols and workflow recommendations.

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The Sequel II systems provide affordable high-quality genome assemblies.

  • Simultaneously generate whole genome and epigenome data by sequencing on a PacBio system

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Data analysis

Assemble genomes with full-solution analytical software tools and standard file formats.

  • Use SMRT Link for fully automated demultiplexing, assembly, circularization, and polishing of both chromosomes and plasmids to produce gold standard references
  • Download and explore HiFi data from high-throughput bacterial whole genome sequencing

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Closed genomes reveal all the variants that drive microbial biology

Researchers from leading German institutes used SMRT sequencing to obtain closed chromosomes and plasmids of Klebsiella pneumoniae ST147 isolates from hospitals, revealing that both SNPs and complex rearrangements contribute to the evolution of antibiotic resistance and virulence. Explore this research further:

Zautner, A. E., et al. (2017). Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing. Journal of Antimicrobial Chemotherapy, 72(10), 2737–2744.


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Gapless assemblies to better understand fungal genomes

A recent study highlighted the potential public health risk posed by historically poor fungal genome assemblies. With PacBio sequencing, it is now possibly to achieve finished yeast genomes, including complete centromeres and telomeric regions. Explore this research further:

Douglass, A. P., et al. (2018). Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS Pathogens, 14(7), e1007138.

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