The One Codex Blog Posts about announcements

One Codex Releases New, Largest Ever Database

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.

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Notebooks (and more!)

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!

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Running new analyses & whole-genome alignments

Today we’d like to tell you about a new feature on One Codex that allows you to run new analyses against your samples, including AMR gene panels and whole-genome alignments. Running New Analyses When samples are uploaded to One Codex, we automatically classify them using the One Codex Database of ~40K complete microbial genomes. However, metagenomic classification is just one of a range of microbial analysis tools provided by the One Codex platform.

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2.0!

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.

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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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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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