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FastQC after Adapter Removal Specifications

Process Details

  • Name: FastQC after Adapter Removal
  • Process UUID: U6mDcKCurbGcnnPASyNwfDfCh3lJNn
  • Process Group: QC

Overview

FastQC after Adapter Removal is a quality control process that performs comprehensive quality assessment of sequencing data following adapter removal procedures. This process aims to provide a simple way to perform quality control checks on processed sequence data from high throughput sequencing pipelines, ensuring that adapter removal has been successful and the remaining sequences meet quality standards for downstream analysis.

This process is implemented in Bash.

Key Functionality

  • Quality Assessment: Performs comprehensive quality control analysis on FASTQ files after adapter sequences have been removed
  • HTML Report Generation: Creates detailed HTML reports with quality metrics, base quality scores, sequence composition, and potential contamination detection
  • Post-Processing Validation: Validates that adapter removal procedures have been successful and identifies any remaining quality issues

Input/Output Specification

Inputs

Required Inputs

  • Mate Information

    • Description: Metadata indicating paired-end sequencing mate information for proper processing
    • Format: mate

  • Processed Reads

    • Description: High-throughput sequencing reads that have undergone adapter removal processing
    • Format: fastq

Outputs

  • FastQC Report
    • Description: Comprehensive quality control report containing quality metrics, base composition analysis, sequence duplication levels, and potential contamination assessment
    • Format: html

Parameters & Settings

This process uses conditional execution parameters that are configured at the pipeline level to determine when FastQC analysis should be performed after adapter removal.

References & Resources

  • Tool Documentation: FastQC is a widely-used bioinformatics tool. Official documentation is available 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