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Genome Annotation

subworkflows/local/annotate_genomes

Steps

  1. Genome annotation is performed using Bakta within bakta_annotate.nf

    • You must download a Bakta database and add its path to the nextflow.config file or add its path as a command line option
    • To skip running Bakta add --skip_bakta true to your command line options.

  2. Screening for antimicrobial resistance Abricate is used with the default options and default database, however you can specify a database by updating the args in the nextflow.config for Abricate.

    • You can skip running Abricate by adding --skip_abricate true to your command line options.

  3. Screening for plasmids is performed using Mob-suite with default options.

  4. Selection of Pointfindr database. This step is only ran if running StarAMR. It will try and select the correct database based on the species identified earlier in the pipeline. If a database cannot be determined pointfinder will simply not be run.

  5. Exporting of StarAMR databases used. To provide a method of user validation for automatic database selection, the database info from StarAMR will be exported from the pipeline into the file StarAMRDBVersions.txt and placed in the StarAMR directory.

  6. Screening for antimicrobial resistance with StarAMR. StarAMR is provided as an additional option to screen for antimicrobial resistance in ResFinder, PointFinder and PlasmidFinder databases. Passing in a database is optional as the one within the container will be used by default.

    • You can skip running StarAMR by adding the following flag --skip_starmar

NOTE: A custom database for Bakta can be downloaded via the commandline using bakta_download_db.nf. The bakta_db setting can be changed in the nextflow.config file, see bakta

Input

  • Contig file (fasta) from the FinalAssembly dir
    • This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)
  • metadata from prior tools

Output

  • Assembly
    • Annotation
      • Abricate
      • Mobsuite
        • recon
          • SAMPLE
      • StarAMR
        • SAMPLE