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FastQC post Specifications

Process Details

  • Name: FastQC_post
  • Process UUID: f9318545z71w8b8cq6mtt6umii9sr4
  • Process Group: Pre_Processing

Overview

FastQC post provides comprehensive quality control visualization and statistical analysis of sequencing reads after processing steps have been completed. This process generates detailed HTML reports containing quality metrics, sequence composition analysis, and potential issues identification to assess the final quality of processed sequencing data.

This process is implemented in Bash, utilizing the FastQC bioinformatics tool for quality assessment.

Key Functionality

  • Quality Control Assessment: Performs comprehensive quality analysis of processed FASTQ files
  • Statistical Reporting: Generates detailed quality metrics and statistics for sequencing data
  • HTML Visualization: Creates interactive HTML reports with graphical quality control summaries
  • Multi-threaded Processing: Utilizes parallel processing to efficiently analyze paired-end sequencing files

Input/Output Specification

Inputs

Required Inputs

  • reads
    • Description: Set of FASTQ files containing sequencing reads for quality assessment
    • Format: FASTQ

Outputs

  • outputHTML
    • Description: HTML report containing comprehensive quality control metrics, visualizations, and statistical summaries of the sequencing data
    • Format: HTML

Parameters & Settings

This process uses system-configured parameters and does not expose user-configurable options in the Foundry UI.

References & Resources

  • Tool Documentation: FastQC official documentation at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • Related Papers: Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc