Viewing 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.
The Genome Report can be downloaded by clicking the download icon in the top left of the screen when the report is in view.
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. The report's cluster section will be first need initialising by clicking the "Cluster Now" button. This will begin a search for near neighbours according to 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.
Once the search is complete, the genomes clustered with the query genome are displayed in the interactive embedded cluster viewer. Below the clusters, a slide bar shows the number of linked genomes at different thresholds, up to the maximum of 50 differences. Selecting different thresholds will display the genomes at that threshold. For more details on how to use the see the section on Genomic Neighbourhood Search. The "View Clusters" button opens up the clustering in the "Cluster Viewer".
The "Re-cluster" button re-runs the neighbourhood search, adding any new genomes that have been added to the public set, or those that the user has access to via sharing or directly uploading.
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