Context search overview

The basic of how the search tool works

About cgMLST-based Neighbour Finding

For species where there is a cgMLST scheme available, we also provide a single-linkage clustering-based service for finding clusters based on a specified threshold. This helps to identify similar sequences which could be indicative of a transmission event or outbreak. The cgMLST search tool can be found in the genome reports and collection views (experimental). For technical details about how cgMLST allele and ST codes are assigned, follow the links to the cgMLST and clustering documentation.

Click on the genome name in any view to pop up the Genome Report and, if there is a cgMLST scheme available, the clustering panel will be visible in it.

Pipeline Overview

The search tool runs in three stages:

1. Compare cgMLST profiles to find 5000 nearest neighbours to the query genome(s).

2. Run an all-v-all comparison to create a distance matrix.

3. Generate single linkage clusters using the selected threshold.

Note that due to the single linkage clustering, individual pairwise distances may be greater than the threshold.

Results

All genomes clustered to the query genome(s) are returned. Only genomes available to individual users are used in the search clustering. Your private uploads are not available to other users in any form. The functions available upon generating your context depends on whether this is done in the genome reports or collection views.