The One Codex Blog

Cautious Metagenomics: A Story of Anthrax in the NYC Subway

Ok, anthrax might sound a bit scary, but this is a story about something that should make you feel good. Wait, is that really Anthrax? Back in the Spring of 2015, researchers studying the microbial ecology of the built environment generated a very large amount of genomic data from microbes found in the New York City subway system. To give you some idea of the magnitude, they generated 10.4 billion sequence reads across 1,457 samples.

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Automated MLST annotation

Today we added automated Multi-Locus Sequence Typing (MLST) to One Codex. MLST is a powerful epidemiological tool that is based on curated collections of conserved mutations in core marker genes. This common reference standard is used to differentiate closely-related isolates of the same species, with many common species having hundreds or thousands of defined MLST profiles. Datasets that are identified as being isolates or single-genome assemblies will be automatically analyzed and tagged with the detected ST label.

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Launching out of beta!

Today is a big day for One Codex, where we’re launching out of beta! This marks the introduction of a number of new features (and many under-the-hood improvements), and incorporates much of the feedback our users have provided this year. You will notice some changes to our website, and the platform can now be found at app.onecodex.com (note that all previous links to the beta site will still work).

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Sample comparison tool

Today we’re launching our new sample comparison tool on the One Codex Beta Platform. The tool enables quick selection and comparison of any of your samples and displays the abundance of taxonomic groups in each sample as a stacked bar graph: The comparison view supports large side-by-side comparisons, viewing data at a particular taxonomic level and/or abundance, filtering to specific clades, and relative vs. absolute scaling modes. See an example and try out the tool here

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Instant sequence search

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.

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Larger, improved reference libraries

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.

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Public links and a better datasets view

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.

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CDC "No-Petri-Dish" Challenge

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).

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