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Ctg Name Edit Specifications

Process Details

  • Name: ctg_name_edit
  • Process UUID: f931yghz9thkmehg4z105wl00hkmrf
  • Process Group: MAG-qc

Overview

This process performs contig header name editing for FASTA files containing metagenomic assembled genomes (MAGs). The process ensures that contig headers do not exceed 38 characters in length, which is a requirement for downstream annotation tools like Prokka. Headers that exceed this limit are automatically truncated to prevent processing errors.

This process is implemented in Bash.

Key Functionality

  • Header Length Validation: Checks if FASTA headers exceed 38 characters in length
  • Automatic Truncation: Truncates headers longer than 38 characters to exactly 38 characters
  • File Organization: Organizes processed FASTA files into a structured directory hierarchy for downstream processing
  • Batch Processing: Processes multiple FASTA files in a single operation

Input/Output Specification

Inputs

Required Inputs

  • FASTA File Set
    • Description: Collection of FASTA files containing metagenomic assembled genomes with potentially long contig headers
    • Format: FASTA (.fa)

Outputs

  • FASTA File Set
    • Description: Processed FASTA files with contig headers truncated to 38 characters maximum, organized in prokka/bins directory structure
    • Format: FASTA (.fa)

Parameters & Settings

This process does not have user-configurable parameters.

References & Resources

  • Tool Documentation: This process uses standard Unix text processing utilities (awk, mv) for header manipulation