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bacterial_genome_annotation

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

  • Author(s):
  • ABRomics
  • abromics-consortium
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.6
  • License: GPL-3.0-or-later
  • UniqueID: d55a9e46-a205-4143-b92f-3783499063ed

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