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MultiQC Specifications

Process Details

  • Name: MultiQC
  • Process UUID: cAfaawQSrPpRh3oXKLwvG3pS3IQUXV
  • Process Group: QC

Overview

MultiQC is a quality control aggregation tool that creates comprehensive summary reports from multiple bioinformatics analysis outputs. This process collects and consolidates quality metrics from various upstream analyses into a single, interactive HTML report for streamlined quality assessment across samples and analysis steps.

This process is implemented in Bash.

Key Functionality

  • Multi-tool Integration: Aggregates quality control metrics from multiple bioinformatics tools including alignment, quantification, and quality assessment outputs
  • Interactive Reporting: Generates comprehensive HTML reports with interactive plots and tables for easy interpretation of quality metrics
  • Comprehensive Analysis: Processes outputs from RSEM quantification, alignment statistics, and other quality control tools to provide a unified view of data quality

Input/Output Specification

Inputs

Required Inputs

  • Text Files

    • Description: Quality control output files in text format from various analysis tools
    • Format: txt

  • RSEM Output

    • Description: Gene expression quantification results from RSEM analysis
    • Format: rsemOut

  • Analysis Output Files

    • Description: Standard output files from various bioinformatics analyses
    • Format: out

  • TSV Files

    • Description: Tab-separated value files containing quality metrics and statistics
    • Format: tsv

  • HTML Reports

    • Description: HTML-formatted quality control reports from individual tools
    • Format: html

  • Bowtie Output

    • Description: Alignment statistics and results from Bowtie aligner
    • Format: bow

  • Results Directories

    • Description: Complete results directories containing multiple output files from analysis pipelines
    • Format: results

  • Output Directories

    • Description: Directory structures containing organized analysis outputs
    • Format: directory

Outputs

  • MultiQC Report
    • Description: Comprehensive HTML report containing aggregated quality control metrics, interactive plots, and summary statistics from all input analyses
    • Format: html

Parameters & Settings

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

  • MultiQC Parameters
    • Description: Optional multiqc parameters
    • Default value: (empty)

References & Resources

  • Tool Documentation: MultiQC is a widely-used bioinformatics tool. For detailed documentation, visit the official MultiQC website at https://multiqc.info/
  • Related Papers: Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047-3048. doi:10.1093/bioinformatics/btw354