Genome Reports

Detailed reports on individual assemblies.

Genome Reports

A detailed report on each assembly can be accessed from the Genome tab or from within the Cluster or Collection views by clicking on the assembly name. The assembly 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.
Clicking the printer icon in the corner will generate a printable version of the report.

Core genome-based neighbourhood searches

From here the cgMLST-based clusters can also be accessed. For species where a cgMLST scheme exists, a "Clusters" section will appear in the report. 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.