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gtdbtk get mag refs Specifications

Process Details

  • Name: gtdbtk_get_mag_refs
  • Process UUID: f931mr5vlf9dbthsjzrl9yd536ciwa
  • Process Group: MAG-qc

Overview

This process performs taxonomic classification of Metagenome-Assembled Genomes (MAGs) followed by comparative genomics analysis. It first uses GTDB-Tk to classify MAGs taxonomically against the Genome Taxonomy Database (GTDB), then pairs each MAG with its closest reference genome based on GTDB taxonomy. Finally, it employs the dnadiff tool to perform detailed genomic comparisons between each MAG and its corresponding reference genome, generating comprehensive reports of genomic differences and similarities.

This process is implemented in Bash, which invokes a Python script for MAG reference pairing and uses GTDB-Tk and dnadiff for taxonomic classification and genomic comparison respectively.

Key Functionality

  • Taxonomic Classification: Classifies MAGs using GTDB-Tk against the comprehensive GTDB reference database
  • Reference Genome Pairing: Automatically identifies and pairs each MAG with its closest reference genome based on taxonomic classification
  • Comparative Genomics Analysis: Performs detailed genomic comparisons using dnadiff to identify structural differences, SNPs, and indels between MAGs and reference genomes

Input/Output Specification

Inputs

Required Inputs

  • gtdbDatabase

    • Description: GTDB reference database for taxonomic classification
    • Format: gtdb

  • fastaFile

    • Description: Set of MAG sequences to be classified and compared
    • Format: fasta

Outputs

  • OutTXTset

    • Description: Set of text files containing detailed comparison reports and analysis outputs
    • Format: txt

  • fastaSet

    • Description: Set of reference genome sequences corresponding to the closest matches for each input MAG
    • Format: fa

  • outFileTSV

    • Description: Taxonomic classification summary table from GTDB-Tk analysis
    • Format: tsv

References & Resources

  • Tool Documentation: Contact the team for details on get_mag_refs.py
  • Related Papers:
  • Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36(6):1925-1927. doi:10.1093/bioinformatics/btz848