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Call ORFs Specifications

Process Details

  • Name: call_orfs
  • Process UUID: f931xfn0u0p35j2l7b5sqz1p249s8d
  • Process Group: Binning

Overview

This process annotates bacterial genomes from Metagenome-Assembled Genomes (MAGs) by detecting and annotating short open reading frames (sORF). The process performs comprehensive genome annotation including gene prediction, functional annotation, and metabolic pathway analysis using the Bakta annotation pipeline.

This process is implemented in Bash, which invokes the Bakta tool for bacterial genome annotation.

Key Functionality

  • Open Reading Frame Detection: Identifies and predicts protein-coding sequences in bacterial genomes
  • Functional Annotation: Assigns functional descriptions and database cross-references to predicted genes
  • Metabolic Pathway Analysis: Maps genes to metabolic pathways and biological processes
  • Database Integration: Utilizes comprehensive reference databases for accurate annotation

Input/Output Specification

Inputs

Required Inputs

  • Fasta File

    • Description: Bacterial genome sequences from MAGs in FASTA format
    • Format: fasta

  • Bakta Database

    • Description: Reference database containing protein sequences, functional annotations, and taxonomic information for bacterial genome annotation
    • Format: baktadb

Outputs

  • Output File TSV

    • Description: Tabular annotation results containing gene predictions, functional assignments, and database cross-references
    • Format: tsv

  • Fasta

    • Description: Annotated genome sequences with predicted open reading frames
    • Format: fasta

  • Log Output

    • Description: Process execution log containing runtime information and annotation statistics
    • Format: out

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Bakta Database Path
    • Description: Path to the Bakta reference database for annotation
    • Default value: (empty string - requires user specification)

References & Resources

  • Tool Documentation: Contact the team for details on the Bakta annotation pipeline
  • Related Papers: Schwengers, O., Jelonek, L., Dieckmann, M.A. et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment and homology based inference. Microb Genom. 2021;7(11):000685. doi:10.1099/mgen.0.000685