The One Codex Blog

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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Detecting Antimicrobial Resistance in Foodborne Pathogens

Today we’d like to tell you about a set of panels on One Codex designed to help detect antimicrobial resistance (AMR) in two important foodborne pathogens – Escherichia coli and Campylobacter coli / C. jejuni. AMR in E. coli and Campylobacter coli / C. jejuni Antibiotic resistant infections are a huge challenge for modern healthcare, and there is a global effort underway to improve our identification and treatment of these hardy infections.

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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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New features: Whole genome clustering and BaseSpace integration

Today we’re happy to announce two new features for all users on One Codex: whole genome clustering and integration with Illumina’s BaseSpace. The first opens the door to new types of analyses, while we hope the second will allow many to spend less time moving their data around and more time exploring it! Whole (meta)genome clustering In addition to our previous sample comparison tool, we’re very excited to announce that One Codex now supports arbitrary, interactive exploration and clustering of your isolates and metagenomic samples.

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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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