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Summarize Reports Specifications

Process Details

  • Name: Summarize Reports
  • Process UUID: f931v75ycpvb3tle2ud3pco8632pd2
  • Process Group: MAG-qc

Overview

This process combines and summarizes all the QC metrics and reports for each sample into a single CSV file for each sample. It aggregates quality control data from multiple bioinformatics tools including CheckM2, strain heterogeneity analysis, MAG relative abundance, GUNC contamination assessment, GTDB-Tk taxonomic classification, DNA difference analysis, QUAST assembly statistics, and Prokka annotation results into a comprehensive summary report.

This process is implemented in Bash, which invokes a Python script for data aggregation and report generation.

Key Functionality

  • Multi-tool QC Integration: Combines quality metrics from eight different bioinformatics analysis tools into a unified report
  • Sample-level Summarization: Generates individual comprehensive CSV summary files for each analyzed sample
  • Quality Assessment Compilation: Aggregates assembly quality, contamination, taxonomic classification, and annotation statistics
  • Standardized Output Format: Produces consistently formatted CSV reports for downstream analysis and visualization

Input/Output Specification

Inputs

Required Inputs

  • Input File TSV

    • Description: Primary TSV input file containing sample metadata or initial quality metrics
    • Format: TSV

  • CSV File

    • Description: Additional CSV input file with supplementary quality control data
    • Format: CSV

  • Output File TSV Sets

    • Description: Collection of TSV files from various QC analysis tools (CheckM2, strain heterogeneity, MAG relative abundance, GTDB-Tk, DNA difference analysis)
    • Format: TSV

Outputs

  • CSV Output
    • Description: Comprehensive summary CSV file containing consolidated QC metrics and reports for each sample
    • Format: CSV

References & Resources

  • Tool Documentation: Contact the team for details on summarize_reports.py