The One Codex Blog

We’ve just released a new Report designed specifically for analyzing the data from the Ampliseq™ Antimicrobial Resistance Community Panel. Now, when you upload sequencing data for this panel generated on either the Illumina or Ion platform, One Codex will automatically detect and analyze the data for you. The output is a PDF report showing exactly which AMR markers appear to be present in your data, all laid out in an easily interpretable format.

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.

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:

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. We’ve increased coverage of all branches of the tree of life, with nearly 1,700 fungal genomes, another 1,700 archaeal genomes, 27,000 viruses, and more than 53,000 bacteria. Collectively, this database provides the most comprehensive snapshot of complex microbial samples.

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: