One Codex

One Codex operates as a data platform for applied microbial genomics, providing bioinformatics solutions for metagenomics and microbial genomics. Founded in 2014 by Nick Greenfield, the company originated from the Y Combinator accelerator program with the goal of helping scientists analyze complex microbial genomic samples. Greenfield, a self-described software and data nerd, transitioned from management consulting to technology before founding One Codex, bringing a background in software engineering and data science to the company's mission. The company's journey includes an acquisition by Invitae (NVTA) in February 2021 for $83.4 million, followed by a spin-out as an independent entity through an employee-led buyout in September 2022.

The company's core business revolves around its web-based platform that enables researchers to upload sequencing data (in FASTA or FASTQ format) and receive rapid, comprehensive analysis. This service caters to a diverse client base, including academic laboratories, biotechnology companies developing live biotherapeutics, and clinical laboratories focused on infectious disease diagnostics. One Codex generates revenue through different pricing structures for academic and commercial clients and also offers end-to-end services that include sample preparation and shotgun metagenomic sequencing. The business model focuses on making complex genomic data accessible and interpretable for both bench scientists and computational biologists.

The One Codex platform is distinguished by its use of a vast, curated microbial reference database for taxonomic classification. It utilizes a k-mer-based taxonomic classification algorithm to identify microbial sequences, including bacteria, viruses, fungi, and protozoa. Key features of the platform include taxonomic classification to the species level, functional prediction to identify markers like antimicrobial resistance, and the ability to generate reproducible reports in various formats. For advanced users, the platform integrates Jupyter Notebooks for custom analyses on a large scale. Beyond its analytical software, One Codex also provides a full microbiome sequencing service, which includes DNA extraction and library preparation, offering clients a complete sample-to-answer workflow. The platform is built on Amazon Web Services and is designed to be secure, offering HIPAA-level security for handling sensitive data.

Keywords: microbial genomics, metagenomics, bioinformatics platform, microbiome analysis, genomic sequencing, taxonomic classification, infectious disease diagnostics, biosecurity, DNA sequencing analysis, shotgun sequencing, microbial database, next-generation sequencing, live biotherapeutics, clinical diagnostics, pathogen detection, data platform, genomic surveillance, functional genomics, bioinformatics solutions, microbiome research