EnteroBase tutorials and worked examples

Here we provide step by step walkthroughs with real datasets that will guide you EnteroBase’s major features. Some of these datasets are presented in Zhou et al, bioRxiv 613554

Case study - Agama

The initial tutorials focus on a specific rare Salmonella serovar called Agama. Salmonella encompasses more than 1,586 defined serovars, with many being rare and poorly understood. By codifying an entire genus (Salmonella in this case), EnteroBase allows rapid analysis of the population structure of even rare serovars. EnteroBase also allows you to look at both diversity within a limited local geographical area and compare this to the diversity all over the world.

Our first tutorial will take you through the main interface and basic searches using EnteroBase with Agama as an example.

The second tutorial introduces User Space OS. Creating datasets through workspaces and sharing them with collaborators form a central part of staying organised on EnteroBase, which you can read about here.

Deeper concepts underpinning EnteroBase

We also recommend reading about representing population structure using MLST, rMLST and cgMLST here. This is how populations are classified in EnteroBase, and will help you quickly navigate genetic relationships between strains.

Since late 2018, we have expanded the MLST/rMLST/cgMLST concepts with Hierarchical Clustering of cgMLST STs (HierCC), a novel approach which supports analyses of population structures at multiple levels of resolution. Both the HierCC method and how to use it are described here.

Best practice for managing your data

The amount of data can quickly get overwhelming. We have a few tutorials on how to better curate and manage your data. For instance, there are many cases where the same strain may have data from different sources, which you would want to combine. In EnteroBase these are managed through Uberstains/substrains relationships, which you can read about here.

This tutorial will show you how to edit standard metadata in EnteroBase, particular for data you own.

Visualisation tools

  • EnteroBase includes GrapeTree, which is explained here.
  • And the SNP Project/Dendrogram, which is covered here.

Inner mechanics of EnteroBase

EnteroBase is a sprawling web resource with many internal components. These components and how they interact with each other and the wider world are explained here.