Genome Reports

Detailed reports on individual genomes.

Genome Reports

Each genome has a detailed report associated with it, comprising its metadata and analysis outputs. The information in the report match the data in the Data Tables, with extra details added. The report can be accessed by clicking on the genome's name (leftmost column, purple) in the Data Tables.

The report includes detailed results for each tool run by Pathogenwatch, e.g. MLST or Genotyphi, along with metadata and assembly metrics such as N50. The version of each tool is also tagged, and a link to the original FASTA provided at the top. Most of the information in the report is also shown in the Data Tables.

To better understand the data included in the Genome Report, refer to the relevant Analysis Tools pages.

Example pages of a Genome Report

The Genome Report can be downloaded by clicking the download icon in the top left of the screen when the report is in view.

Download Genome Report as PDF

Core genome-based neighbourhood searches

For species where a cgMLST scheme exists, the cgMLST-based clusters can be accessed from within the genome report. In these cases, a "Core Genome Clustering" section will appear in the report. When you scroll to the clustering section, the genome's cluster is loaded from the server. The Re-cluster button re-runs the clustering container to update the clustering cache document, searching for near-neighbours within both yours and any public genomes, and creating a set of single-linkage clusters according to the specified cgMLST allele similarity threshold. The "View Cluster" button links to the "Cluster Viewer" page.

Pressing the "Cluster Now" button will search for near-neighbours within both yours and any public genomes, and create a set of single-linkage clusters according to the specified cgMLST allele similarity threshold. For details see the cgMLST-Clusters description. Clicking the link next to a cluster will allow you to view the cluster as a Collection View.