Fig 1.
Flowchart depicting the workflow of the BAP.
The input from the user is assembled if needed, and the bacterial species is identified through the KmerFinder algorithm. When ready, the assembled contigs are submitted to the ContigAnalyzer and ResFinder for annotation of contig metrics and identification of resistance genes. If the bacterial species is identified, the contigs are further, if applicable, submitted to MLST, PlasmidFinder and VirulenceFinder to identify the sequence type, known plasmids (and, if applicable, their plasmid sequence type), and known virulence genes. When all services are done, the BAP produces a summary report of the services result (see Fig 2).
Fig 2.
Example of a BAP summary report for a S. aureus sample.
The report is split in 3 parts: Contigs/assembly analysis, taxonomy analyses and phenotypic analyses. Only the major result details are shown here, but the user is provided direct links to see the full report from the individual services.
Table 1.
List of the seven mandatory metadata fields from the CGE metadata template.
Fig 3.
Snippet from the result data for the MLST dataset.
The list shows a small selection of the metadata associated with each sample. The column headers are marked in bold and the headers for the services' result are marked with the 'r_' prefix.
Fig 4.
KmerFinder top results for sample S. aureus F38.
The result shows that there are more than just significant hits for S. aureus. This indicates that the sample was contaminated and thus not a single isolate.
Table 2.
Assembly by the internal Assembler.
Table 3.
Species prediction by KmerFinder.
Table 4.
Sequence type prediction by the MLST algorithm.
Table 5.
Resistance gene prediction by the ResFinder.
Table 6.
Virulence gene prediction by the VirulenceFinder.
Table 7.
Plasmid prediction by the PlasmidFinder algorithm.
Table 8.
Plasmid sequence type prediction by the pMLST algorithm.