The One Codex Blog

SARS-CoV-2, the virus responsible for the disease COVID-19, is now widespread within our communities and has personally affected members and friends of our team.

In an effort to contribute however we can, our team has been working to make analysis of genomics data from COVID-19 samples simpler, more accessible, and easier to share with the broader community. Today, we’re announcing a new analysis summarizing the detection of SARS-CoV-2 in samples that contain evidence of the virus. We’re making this analysis available at no charge and it will be automatically run on any samples in which we detect SARS-CoV-2. In return, all that we ask is that you share relevant metadata and the consensus sequences from your samples (and we’ll help enable that).

The One Codex and ATCC teams have been hard at work improving the ATCC Genome Portal. Since launching 6 months ago, we’ve more than doubled the number of genomes on the portal (adding more than 300 new genomes on top of our original 250) and created new features to help you navigate our collection of high-quality reference genomes. In this post, we’ll show you our new Gold genomes, help you browse the collection by tag, and show you how to access more granular contig details for each of our genomes.

In this post we take a look at a new paper from Eli Moss, Dylan Maghini, and Ami Bhatt that describes a new approach for assembling complete genomes using Oxford Nanopore’s MinION sequencer. Read on to find out more!

The new ATCC Genome Portal offers high-quality, authenticated genomes and annotations for many of the top items in ATCC’s catalog. Today, the portal includes over 365 closed, fully circularized bacterial genomes from ATCC’s collection. That’s 1 genome sequenced and closed per day in 2019! And we’re continuing to generate more data every month.

We’re always working hard to make it as easy as possible to get the quality results from your microbiome data. Today we’re rolling out a brand new feature called Smart Detection.

We’ve traditionally run our standard One Codex Database analysis on all samples that have been uploaded. Sometimes, though, that just isn’t the best analysis to run. If you have amplicon data or Ion Ampliseq™ data for example, it makes more sense to run our Targeted Loci analysis or our new Ion Ampliseq™ AMR panel.