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Prokka Ctg Specifications

Process Details

  • Name: prokka_ctg
  • Process UUID: f93178vj0mpl53av6f0eceabihut72
  • Process Group: MAG-qc

Overview

This process performs automated prokaryotic genome annotation using Prokka, a rapid prokaryotic genome annotation tool. It processes FASTA files containing bacterial contigs or genomes and generates comprehensive annotations including gene predictions, functional annotations, and feature summaries. The process is designed for quality control and characterization of Metagenome-Assembled Genomes (MAGs).

This process is implemented in Bash.

Key Functionality

  • Prokaryotic Gene Prediction: Identifies and predicts protein-coding sequences, tRNAs, rRNAs, and other genomic features in bacterial genomes
  • Functional Annotation: Assigns functional annotations to predicted genes using multiple databases and tools
  • Batch Processing: Processes multiple FASTA files in parallel, generating organized output directories for each genome
  • Quality Control Integration: Provides standardized annotation output suitable for MAG quality assessment workflows

Input/Output Specification

Inputs

Required Inputs

  • fastaFile
    • Description: Set of FASTA files containing bacterial contigs or assembled genomes to be annotated
    • Format: FASTA (.fa)

Outputs

  • OutTXTset

    • Description: Set of text files containing detailed annotation summaries and statistics for each processed genome
    • Format: TXT

  • outFileTSV

    • Description: Tab-separated value files containing structured annotation data including gene coordinates, functional assignments, and feature classifications
    • Format: TSV

Parameters & Settings

This process uses fixed parameters optimized for bacterial genome annotation. The kingdom is set to "Bacteria" and the process utilizes available CPU threads for parallel processing.

References & Resources

  • Tool Documentation: Prokka is a well-established prokaryotic genome annotation pipeline. For detailed information about Prokka's annotation methodology and output formats, refer to the official Prokka documentation.
  • Related Papers: Seemann T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30(14):2068-2069. doi:10.1093/bioinformatics/btu153