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Quality Filtering Summary Specifications

Process Details

  • Name: Quality Filtering Summary
  • Process UUID: 17fc6140-e169-11e9-be30-e0aab38271b1
  • Process Group: Summary

Overview

This process parses quality filtering log files generated by fastx and Trimmomatic tools to create a comprehensive summary table for reporting purposes. It extracts read count statistics before and after quality filtering operations, providing essential quality control metrics for sequencing data analysis workflows.

This process is implemented in Perl.

Key Functionality

  • Log File Parsing: Automatically detects and processes both fastx_quality.log and trimmomatic_quality.log files in the working directory
  • Read Count Extraction: Extracts total input reads and reads remaining after quality filtering from log files
  • Paired-End Support: Handles both single-end and paired-end sequencing data with appropriate read count calculations
  • Summary Table Generation: Creates a structured TSV file containing quality filtering statistics for all processed samples

Input/Output Specification

Inputs

Required Inputs

  • Log File

    • Description: Quality filtering log files from fastx or Trimmomatic tools
    • Format: log

  • Mate

    • Description: Sequencing type specification (single-end or paired-end)
    • Format: mate

Outputs

  • Output File TSV
    • Description: Summary table containing sample names, total reads, and reads after quality filtering
    • Format: tsv

References & Resources

  • Tool Documentation: Contact the team for details on the Perl script implementation