One Codex is a data platform for applied microbial genomics, enabling new and valuable applications in clinical diagnostics, food safety, and biosecurity

Best-in-class metagenomics

One Codex helps applied microbiologists rapidly assess their samples, with a platform that is:

Fast – Process isolates or complex metagenomic samples in minutes, not days

Comprehensive – Search the world's largest index of bacterial, viral, and fungal genomes

Accurate – Sensitivity and precision comparable to or greater than today's leading methods

In silico panels

In silico gene or marker panels offer a functional window into an NGS sample, including predicted virulence factors, antibiotic resistance, and other phenotypic traits

These panels complement metagenomic analysis with specific, easy-to-interpret assays

Microbial genomics — in context

Rich sample management allows complex samples to be indexed, searched, and compared

Organize + query samples

Search for samples by name, metadata, MLST, tag, or the taxa present and concentration

Compare analyses

Simple, but powerful sample comparison, including exportable data, taxa filtering, and drilldown

Plans & pricing


  • Up to 50 private samples
  • Command-line and API access
  • Best-in-class metagenomic analyses
  • Sample management and search
  • 100% reproducible workflows
  •  No commercial use or support


  • All Research features and
  • 100's or 1000's of private samples
  • Custom references + workflows
  • HIPAA compliance
  • Audit logs for all analyses
  • Premium support + custom SLAs

Academic user?  Researchers are entited to the Research plan above with 100 private samples, plus unlimited public samples for collaborating projects. Need assistance, more samples, or want to discuss a collaboration? Please send us a note.

Need sequencing too?  We can also provide sequencing for many types of samples – contact us to discuss your needs.