Bacterial genome annotation workflow (v1.0)

This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:

1. Genomic annotation
   • Bakta to predict CDS and small proteins (sORF)
2. Integron identification
   • IntegronFinder2 to identify CALIN elements, In0 elements, and complete integrons
3. Plasmid gene identification
   • Plasmidfinder to identify and typing plasmid sequences
4. Inserted sequence (IS) detection
   • ISEScan to detect IS elements
5. Aggregating outputs into a single JSON file
   • ToolDistillator to extract and aggregate information from different tool outputs to JSON parsable files

Inputs

1. Assembled bacterial genome in fasta format.

Outputs

1. Genomic annotation:
   • genome annotation in tabular, gff and several other formats
   • annotation plot
   • nucleotide and protein sequences identified
   • summary of genomic identified elements
2. Integron identification:
   • integron identification in tabular format and a summary
3. Plasmid gene identification:
   • plasmid gene identified and associated blast hits
4. Inserted Element (IS) detection:
   • IS element list in tabular format
   • is hits in fasta format
   • ORF hits in protein and nucleotide fasta format
   • IS annotation gff format
5. Aggregating outputs:
   • JSON file with information about the outputs of Bakta, IntegronFinder2, Plasmidfinder, ISEScan