We’re pleased to announce that we’re launching a new feature on One Codex today: instant sequence search.

With this new tool, simply enter a nucleotide sequence – whether a read from a FASTQ file or a section of a reference genome – and we’ll instantly compare it against our One Codex database.

How it works

Our instant classifier works by splitting up the input sequence into all overlapping k-mers and then comparing each against our reference database, using a k=31. We then visually highlight the most specific taxonomic value (or lowest common ancestor) for the k-mer in our database. (Note that because the k-mers overlap, we only color the first character of each)

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.

This week, we’re excited to announce a few improvements to help you to better organize and share your data on the One Codex beta platform.

First, you can now make individual samples public, at which point you can share an analysis with anyone (and, of course, you’re always able to make the sample private again too). Here’s a sample public analysis.

Second, we’ve added the ability to both sort and filter your samples in the main datasets view. This is particularly useful for some of our users who are beginning to accumulate large numbers of samples.

We’re excited to announce that the CDC’s Advanced Molecular Detection initiative has named One Codex as the winner of its $200K “No-Petri-Dish” Challenge! We are thrilled to be recognized by a world-leading public health agency and excited to begin offering solutions for next-generation public health and epidemiology.

The “No-Petri-Dish” Diagnostic Test Challenge asked participants to develop a fast “straight-to-strain” method for identifying a type of E. coli known as STEC (a common cause of severe foodborne outbreaks). Current tests available to public health officials fall into two major categories: “culture-based” tests, which require growing a bacterial culture and can take days or weeks to complete; and faster, but significantly less informative tests for specific pathogens or toxins (e.g., PCR-based tests).