Overview

One common use for metagenomic next-generation sequencing (mNGS) is to evaluate patterns across multiple samples. This may involve looking across a cohort of samples and identifying patterns across the cohort, region, or disease phenotype.

In this tutorial, we will explore using IDseq for analysis across multiple samples using the public project Feline Gingivostomatitis. We will learn how to generate heatmaps to compare samples and investigate an outbreak of Feline Gingivostomatitis.

About the Feline Gingivostomatitis Project

This project includes metagenomic sequencing data from oral samples taken from cats at veterinary facilities in the San Francisco Bay Area. The cats fall into two groups: those with and without Feline Gingivostomatitis, a disease characterized by protracted and potentially debilitating oral inflammation in cats.

In this IDseq project, mNGS was used to generate hypotheses regarding the etiology of the disease. By analyzing patterns across multiple cats with similar disease phenotypes, it was possible to hypothesize which pathogen was responsible for the disease.

The main steps in this tutorial are: 

• Creating a Heatmap walks through the steps to find data and create a heatmap for multi-sample analysis.
• Filters & View Settings covers our view settings and ways to filter out the noise in your heatmap.
• Metadata in the Heatmap helps you find patterns among different cohorts in your samples.
• Viewing Sample and Taxon Details covers how to learn more about the samples and taxa details from the heatmap.
• Saving the Heatmap shoes you how to save your heatmap with your settings and filters.