The One Codex Blog

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.

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. Today we’re happy to present some results from an independent academic evaluation.² Using the same datasets and accuracy metrics shows the performance of One Codex is superior to a range of other tools for microbiome analysis.

ASM Microbe, one of the largest microbiology conferences in the world, is right around the corner. With more than 10,000 attendees, it’s a great event to connect with the research community, learn the latest scientific advances, and introduce microbial genomics experts to the One Codex platform you have come to love.

If you are attending the conference, please stop by ATCC’s booths (#2411 & 2413) to meet the One Codex team or send us a note. Here will be launching The ATCC® Microbiome Standards powered by One Codex, which are a set of 6 gDNA and whole cell mixed community standards to measure and improve the accuracy and reliability of microbiome sequencing. We will be providing live demos of the platform, including the scorecard analysis of the ATCC Microbiome Standards. For more information about these products, or more, feel free to email us.

Scientists that study the microbiome generally use two different methods to analyze samples – sequencing all of the DNA in a sample (whole genome sequencing) or targeting a specific marker gene (e.g., 16S, 18S, ITS). While whole genome sequencing (WGS) enables high-resolution taxonomic and functional characterization of microbiome samples, 16S sequencing is a cost effective technique for broad community surveys across large numbers of samples. Today, we’re excited to announce that One Codex is launching a powerful new tool for 16S and other amplicon sequencing – making high-quality, reference-based analysis of marker gene studies easier, faster, and more accessible.

Today, we’re extremely excited to announce several new features we’ve been working on for the past few months. Collectively, these should make it both easier and faster to perform custom, large-scale analyses, explore your data, and build applications atop the One Codex platform:

• A new easier-to-use, more powerful API (read the docs)
• A new version of our command-line interface and an accompanying Python client library for quickly getting started with the new API (take a peek on Github)
• And last but not least – interactive notebooks built directly into the platform!

The new Notebooks feature allows you to launch secure Jupyter (née IPython) notebooks automatically configured for access to your samples and analyses on One Codex. Internally, we’ve already found these incredibly useful for both quick, flexible explorations of metagenomic data as well as more sophisticated, formal analyses.