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Aggregate Quast Specifications

Process Details

  • Name: aggregate_quast
  • Process UUID: f931ecgvinu7c1gdmtiuk4nsi022t2
  • Process Group: MAG-qc

Overview

This process aggregates the quality assessment data across all bins within a sample. It collects individual QUAST reports from multiple directories and combines them into a single comprehensive CSV file for downstream analysis and comparison of metagenome-assembled genome (MAG) quality metrics.

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

Key Functionality

  • Report Collection: Searches through subdirectories to locate individual QUAST report files (report.tsv) from each bin
  • File Renaming: Renames individual reports with directory-specific prefixes to maintain bin identification during aggregation
  • Data Aggregation: Combines all individual QUAST reports into a single consolidated CSV file using the aggregate_quast.py script

Input/Output Specification

Inputs

Required Inputs

  • Output Directory
    • Description: Directory containing subdirectories with individual QUAST reports for each bin
    • Format: Directory

Outputs

  • CSV File
    • Description: Aggregated quality assessment data combining metrics from all bins in the sample
    • Format: CSV

Parameters & Settings

No configurable parameters are available for this process in the Foundry UI.

References & Resources

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