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Gunc Specifications

Process Details

  • Name: gunc
  • Process UUID: f931drlhld8zllczeixeslfbkdcz7e
  • Process Group: Binning

Overview

This process assesses contamination in metagenome-assembled genomes (MAGs) by comparing them against reference genomes using the GUNC (Genome UNClutterer) tool. GUNC detects chimerism and contamination in prokaryotic genomes by identifying genes that consistently co-occur in reference genomes and flagging deviations from these patterns.

This process is implemented in Bash.

Key Functionality

  • Contamination Detection: Identifies potential contamination and chimerism in assembled genomes by analyzing gene co-occurrence patterns
  • Reference Comparison: Compares input genomes against a comprehensive reference database to detect anomalous gene combinations
  • Quality Assessment: Provides quantitative metrics for genome quality and contamination levels
  • Batch Processing: Processes multiple FASTA files simultaneously for efficient workflow integration

Input/Output Specification

Inputs

Required Inputs

  • FASTA Files

    • Description: Set of genome sequences (MAGs) to be assessed for contamination
    • Format: FASTA

  • GUNC Database

    • Description: Reference database containing gene co-occurrence patterns from high-quality genomes
    • Format: DMND (Diamond database format)

Outputs

  • Contamination Report
    • Description: Tab-separated values file containing contamination assessment results, including GUNC scores, contamination predictions, and quality metrics for each input genome
    • Format: TSV

Parameters & Settings

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

  • GUNC Database Path
    • Description: Path to the GUNC reference database file
    • Default value: (empty string)

References & Resources

  • Tool Documentation: Contact the team for details on the GUNC implementation
  • Related Papers: Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S., & Bork, P. (2021). GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biology, 22(1), 178. https://doi.org/10.1186/s13059-021-02393-0