StrainView WHOLE-GENOME SHOTGUN SEQUENCING OF MICROBIAL ISOLATES

Our StrainView™ platform is an ideal high-throughput way to generate draft-level genomes of hundreds or thousands of cultured isolates in parallel.

Compare Microbial Genomes with Whole-genome Shotgun Sequencing

Do you have stored strain-banks of isolated and cultured individual strains for future use in experiments or as potential candidates for use in therapeutics?

StrainView™ allows you to characterize your entire strain collection comprehensively and efficiently.

StrainView™ uses high-coverage DNA sequencing on the Illumina platform followed by genome assembly to produce annotated draft-level assemblies with contigs of hundreds of kilobases.

Our standard StrainView™ assay provides 300 megabases of sequencing data per isolate, equivalent to 60x coverage of a 5 megabase-pair bacterial strain.

CoreBiome’s customers receive an ​interactive online report​ featuring raw data, assembled contigs, comparative genomics visualizations, and annotation of genes and functions including antibiotic resistance genes and virulence factors.

Antibiotic Resistance and Functional Repertoire Annotation

Strains with identical 16S marker genes can have highly divergent metabolic traits and functional content in the rest of their genomes1.

This means that researchers relying on 16S sequences alone to characterize their strain banks may be missing large amounts of potentially important functional diversity.

Historically, a common approach to characterizing strains has been to perform full-length Sanger sequencing on the 16S ribosomal RNA gene.

This approach is affordable and fast, but is limited in what information is provided about any given strain; such as the functional content of that strain’s genome.

CoreBiome’s StrainView™ analysis provides a full characterization of functional content in strains in a high-throughput manner, while also providing taxonomic identity using the entire genome content.

1. Jaspers E, Overmann J. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl. Environ. Microbiol.. 2004 Aug 1;70(8):4831-9.

StrainView™ Basics

Cost:

Starts at $99/strain for 300 megabases per strain.

Minimum order:

88 samples for 3-week turnaround, 24 samples for 6-week turnaround.

Specifications:

Adaptor-removed and filtered sequencing data (fastq), assembled contigs and scaffolds (fasta), genome annotations, inferred taxonomies, antimicrobial resistance profiles, virulence profiles, quality-control dashboard, and a full Core Analysis report. Review example report.

Create a Custom Strain Database for Research

You can also use the StrainView™ isolate genome assembly service to create a fully-annotated custom strain database for your own research purposes.

CoreBiome can include a customer’s isolates in a private, firewalled reference database for use with ​BoosterShot™ ​or ​DeepSeq sequencing projects.

Included in your StrainView™ project are:

  • Initial quality control check on all samples
  • QC report returned for review
  • Amplification and library preparation using our optimized approach
  • Core Analysis Report
    • Genome annotations
    • Taxonomic assignments via fully optimal gapped DNA sequence alignment to a
      curated reference database
    • Antimicrobial resistance profiles
    • Virulence factor profiles
    • Sequencing quality-control dashboard
    • Interactive assembly report
    • Interactive visualizations that leverage your sample metadata
  • Fastqs: adaptor-trimmed and quality-filtered sequencing data
  • Contigs & Scaffolds

Review example report.

StrainView™ sequencing starts at $99 per strain.

To ensure data of the highest quality, we require a minimum number of 24 strains per batch.

Request a quote​ to find out how CoreBiome can help you achieve your scientific goals.

The standard turnaround time for a StrainView™ project is 3 weeks from DNA generation, but we can expedite your results. Find out how by reviewing our FAQ document.

Large projects beyond 1,000 samples may require additional time. Contact us ​with questions.

To ensure your StrainView™ samples return the best data, we recommend performing your DNA extraction​ through CoreBiome.

Input DNA quality and quantity can have dramatic impacts on the microbial profile generated for your samples.

By allowing the experts at CoreBiome to extract and prepare your DNA, we can ensure the best quality library preparations for amplicon sequencing.

We also recommend pelleting isolate samples prior to freezing as this will avoid unintentional dilution of genomic DNA into a liquid storage buffer when cells are lysed during freezing.

For more information regarding sample preparation and shipment, check out our sample guidelines​.

All we need to know are some quick details regarding the types of samples you have, how many, and how they are stored.

From there, our team of experts can recommend the best approach for generating your microbiome data and discoveries.

Request a quote or contact us with questions.

CoreBiome provides services and generates data for research purposes only.

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