The One Codex Blog

Powerful microbiome analysis with Jupyter notebooks

One of the most useful parts of One Codex for our power users is our support for Jupyter notebooks right in the platform. These notebooks let you run arbitrary analyses on your data, without needing to worry about getting your data out of One Codex. We’ve seen users do all kinds of interesting analyses in notebooks, including biomarker detection and machine learning. Today, we’re announcing a significant upgrade to our Notebooks feature that will make creating and sharing interactive reports easier than every.

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One Codex Achieves Highest Overall Score in precisionFDA CFSAN Challenge 🥇

Identifying specific strains and mixtures of strains in complex metagenomic samples is a key challenge in epidemiology, environmental microbiology, and live biotherapeutics development (LBPs). We’ve long been working on this problem and are excited to announce that our in-house strain-calling pipeline recently achieved the highest overall score in the precisionFDA CFSAN Pathogen Detection Challenge. We’re still continuing to hone and test several approaches, but are excited to see that each performed extremely well across the 25+ submissions:

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One Codex Releases New, Largest Ever Database

Today at the Advances in Genome Biology & Technology (AGBT) conference, we are excited to unveil the largest searchable database of microbial genomes. Curated from its larger collection of hundreds of thousands of genomes, the latest One Codex Database includes >80,000 genomes and provides unprecedented sensitivity and specificity for metagenomic applications. The latest One Codex Database enables: Highly sensitive identification of microbes in complex samples Precise quantification of microbial abundances from whole genome sequencing (WGS) data Community-wide characterization of complex microbial samples, including the human microbiome Spanning the tree of life Our latest release includes over 80,000 genomes, representing more than 43,000 distinct species and 69,000 strains across all microbial domains.

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Single Sign-On (SSO) Now Available for Enterprise Customers

Currently, we have several integrations using our APIs. We also integrate with tools, such as BaseSpace for data import. Today, we’re excited to add another new category to our integration landscape, Single Sign-On (SSO) providers, available for our enterprise customers. By integrating One Codex with your SSO provider you will be able to login to your account using your existing corporate credentials; that’s one less password to remember! Here are some additional details:

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Academic Study Data Shows One Codex’s Superior Performance for Metagenomic Analysis

When analyzing microbiome data, it’s very important to know that you are detecting the microbes that are truly present and that the predicted abundances are accurate.1 However, it can be a lot of work to test and validate microbiome analysis tools across a wide range of conditions. We are very grateful to a group of academic researchers from Weill Cornell Medicine, UC-Riverside, IBM, University of Vermont, HudsonAlpha, & Drexel University who performed those evaluations and contributed them to the community.

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