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Umitools Summary Specifications

Process Details

  • Name: Umitools Summary
  • Process UUID: TWnSlA2VS9Yv6cGNw0Fy5vpAm5suSg
  • Process Group: Summary

Overview

This process parses umi_tools log files and creates a summary table for reporting purposes. It extracts key statistics from UMI (Unique Molecular Identifier) processing workflows, including read counts before and after UMI extraction and deduplication steps.

This process is implemented in Perl.

Key Functionality

  • Log File Parsing: Extracts read count statistics from umi_tools log files
  • Deduplication Analysis: Processes deduplication log files when available to track read reduction
  • Summary Table Generation: Creates a comprehensive TSV summary table with all processing statistics
  • Multi-Sample Processing: Handles multiple samples simultaneously for batch analysis

Input/Output Specification

Inputs

Required Inputs

  • Log File

    • Description: umi_tools log file containing processing statistics
    • Format: log

  • Mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

Outputs

  • Output File TSV
    • Description: Summary table containing UMI processing statistics including total reads, reads after UMI extraction, and reads after deduplication (when available)
    • Format: tsv

References & Resources

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