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Init Statistics Specifications

Process Details

  • Name: init_statistics
  • Process UUID: f9311ds3r240wso7brx9m862ear8co
  • Process Group: Pre_Processing

Overview

This process generates comprehensive sample statistics for sequencing data at each preprocessing step. It tracks read counts, quality metrics, and data retention throughout the quality control pipeline, providing essential metrics for monitoring the effectiveness of each preprocessing stage including low-quality read removal, adapter trimming, host sequence removal, and error correction.

This process is implemented in Bash, which invokes Python scripts for read length calculation and statistical summary generation.

Key Functionality

  • Read Statistics Calculation: Computes read counts and length distributions for paired-end FASTQ files at each preprocessing step
  • Multi-step Tracking: Monitors data retention across low-quality removal, adapter removal, host removal, and error correction stages
  • Summary Report Generation: Consolidates statistics from all preprocessing steps into a comprehensive CSV report

Input/Output Specification

Inputs

Required Inputs

  • Mate Information

    • Description: Paired-end sequencing mate designation
    • Format: Value parameter

  • Raw Reads

    • Description: Initial paired-end sequencing reads before preprocessing
    • Format: FASTQ files (compressed)

  • Processed Read Sets

    • Description: FASTQ files from various preprocessing steps (low-quality removal, adapter removal, host removal, error correction)
    • Format: FASTQ files (compressed)

Outputs

  • Statistics Report
    • Description: Comprehensive CSV file containing read counts, quality metrics, and data retention statistics for each preprocessing step
    • Format: CSV

Parameters & Settings

This process runs conditionally based on the pipeline configuration parameter params.run_stats.

References & Resources

  • Tool Documentation: Contact the team for details on calc_read_lens.py and sample_statistics.py