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.

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 excited to announce a major update to One Codex, which includes both improvements to our core metagenomics pipeline and an expansion of our reference database. Along with this update, we’ve also re-analyzed all samples previously uploaded to One Codex (all older analyses of course remain available).

Improved classifier: Better filtering, while maintaining sensitivity

Over the past few years, a number of new k-mer based metagenomic classifiers tools have been developed, including Kraken, GOTTCHA, CLARK, and our own. These methods have enabled ever-larger reference libraries and provided extremely sensitive detection. As a consequence of their design, however, they have also been more prone to false positives than more conservative alignment- or marker-based approaches.

We’re happy to announce that we’ve just released larger, improved microbial reference libraries on One Codex.

More data

The RefSeq Database now includes over 7,000 reference and representative genomes from NCBI, while the One Codex Database holds nearly 34,000 different bacterial, viral, fungal, and archeal genomes. This is more than a 45% and 20% increase, respectively, from the last releases of the RefSeq and One Codex databases. As with all of our data releases, you should continue to see improvements in the specificity of your analyses by using our more comprehensive reference libraries.