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Adapter Removal Summary Specifications

Process Details

  • Name: Adapter Removal Summary
  • Process UUID: 17fc6014-e169-11e9-be30-e0aab38271b1
  • Process Group: Summary

Overview

This process parses adapter removal log files from various tools (fastx and trimmomatic) and creates standardized summary tables for reporting purposes. It aggregates statistics from multiple samples and presents them in a unified tabular format for downstream analysis and quality assessment.

This process is implemented in Perl.

Key Functionality

  • Log File Parsing: Extracts adapter removal statistics from fastx and trimmomatic log files
  • Multi-Tool Support: Handles output from both fastx clipper and trimmomatic adapter removal tools
  • Summary Generation: Creates both basic and detailed summary tables with read counts and filtering statistics
  • Sample Aggregation: Processes multiple samples simultaneously and consolidates results into unified reports

Input/Output Specification

Inputs

Required Inputs

  • Log File

    • Description: Adapter removal log file from fastx or trimmomatic
    • Format: log

  • Mate

    • Description: Sequencing configuration indicating whether data is single-end or paired-end
    • Format: mate

Outputs

  • Output File TSV

    • Description: Basic summary table containing total reads and reads after adapter removal for each sample
    • Format: tsv

  • Output File

    • Description: Detailed summary table with comprehensive statistics including too-short reads, adapter-only reads, non-clipped reads, and N reads (when available)
    • Format: tsv

References & Resources

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