The One Codex Blog

When analyzing microbiome data, it’s very important to know that you are detecting the microbes that are truly present and that the predicted abundances are accurate.¹ However, it can be a lot of work to test and validate microbiome analysis tools across a wide range of conditions. We are very grateful to a group of academic researchers from Weill Cornell Medicine, UC-Riverside, IBM, University of Vermont, HudsonAlpha, & Drexel University who performed those evaluations and contributed them to the community. Today we’re happy to present some results from an independent academic evaluation.² Using the same datasets and accuracy metrics shows the performance of One Codex is superior to a range of other tools for microbiome analysis.

ASM Microbe, one of the largest microbiology conferences in the world, is right around the corner. With more than 10,000 attendees, it’s a great event to connect with the research community, learn the latest scientific advances, and introduce microbial genomics experts to the One Codex platform you have come to love.

If you are attending the conference, please stop by ATCC’s booths (#2411 & 2413) to meet the One Codex team or send us a note. Here will be launching The ATCC® Microbiome Standards powered by One Codex, which are a set of 6 gDNA and whole cell mixed community standards to measure and improve the accuracy and reliability of microbiome sequencing. We will be providing live demos of the platform, including the scorecard analysis of the ATCC Microbiome Standards. For more information about these products, or more, feel free to email us.

Scientists that study the microbiome generally use two different methods to analyze samples – sequencing all of the DNA in a sample (whole genome sequencing) or targeting a specific marker gene (e.g., 16S, 18S, ITS). While whole genome sequencing (WGS) enables high-resolution taxonomic and functional characterization of microbiome samples, 16S sequencing is a cost effective technique for broad community surveys across large numbers of samples. Today, we’re excited to announce that One Codex is launching a powerful new tool for 16S and other amplicon sequencing – making high-quality, reference-based analysis of marker gene studies easier, faster, and more accessible.

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!

The new Notebooks feature allows you to launch secure Jupyter (née IPython) notebooks automatically configured for access to your samples and analyses on One Codex. Internally, we’ve already found these incredibly useful for both quick, flexible explorations of metagenomic data as well as more sophisticated, formal analyses.

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. While in the past we’ve configured additional analyses to run automatically where appropriate (e.g., MLST for common bacterial isolates) or at the request of users, our new Run Analysis page allows you to run an in silico panel or perform whole-genome alignments against any of your samples.