The One Codex Blog

Today, we’re very excited to launch a brand new feature on One Codex that lets you analyze your microbiome data in all new and exciting ways! Custom Plots is a powerful new application for interactively comparing and visualizing your microbiome data across cohorts of many samples.

With Custom Plots, you can explore a variety of different microbiome metrics and plots that were previously only accessible through our Notebooks. This includes taxonomic bar charts (like our current “Quick Compare” tool), alpha diversity plots, and beta diversity plots like heatmaps or Principal Coordinate Analyses (PCoA).

When you’re planning a new study, there are a lot of factors to consider. These can include:

• What population should I target?
• How should I collect and store the samples?
• What analyte do I want to study, and how should I extract it from the samples?
• What kind of technology should I use, PCR, arrays, or sequencing?
• What sequencing approach should I use, amplicon or whole shotgun metagenome?
• How deeply should I sequence?

These are some common questions researchers ask, and your research goals will drive the decisions you make when setting up your study. But there is a commonly underappreciated question, and one that we at One Codex are often asked: how do I know if I have enough samples?

Microbiome studies are complex and require up front planning to ensure you get the data you need to answer your research questions. Poor study design can result in missing differences that exist between cohorts, or worse, it can lead to falsely identifying signals that are unrelated to your research questions. Here, we highlight some of the factors to consider when designing a microbiome study to ensure you get the most out of your study.

One Codex now offers sequencing! Over the years, we’ve heard the same struggles and frustrations from researchers about their microbiome workflow – slow turnaround times, unpredictable costs, high sample minimums, and data that isn’t as reproducible as it should be. We’re excited to share that we now offer shotgun sequencing, including DNA extraction, library prep, sequencing, and bioinformatics on the One Codex platform. For now, we are focused on stool samples, but stay tuned because there is more to come!

Viral metagenomics has become an increasingly important area of study for microbiologists, and it feels especially relevant for 2020 so far. Isolating and sequencing viral DNA or RNA has typically been a tricky and often time-consuming process. We recently partnered with Twist Bioscience to tackle this problem, with the release of the Twist Respiratory Virus Research Panel and One Codex analysis.