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Reads UMIs Assignment Specifications

Process Details

  • Name: readsUMIsAssignment
  • Process UUID: 08f61b91e1334808b494875c5927ffe8
  • Process Group: uminator

Overview

This process assigns sequencing reads to their corresponding Unique Molecular Identifiers (UMIs) by aligning high-quality UMI sequences to the terminal portions of reads. The process performs bidirectional alignment of UMI database sequences to both the beginning and end of reads, filters the alignments based on quality metrics, and bins reads according to their assigned UMIs.

This process is implemented in Bash, which invokes R scripts for UMI filtering and read binning operations.

Key Functionality

  • UMI-to-Read Alignment: Performs BWA alignment of UMI database sequences to both the start and end portions of reads with configurable mismatch tolerance
  • Alignment Quality Filtering: Filters UMI-read alignments based on normalized edit distance statistics to ensure high-quality assignments
  • Read Binning: Groups reads by their assigned UMIs and generates organized output directories for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • inputDir

    • Description: Directory containing candidate UMI extraction results
    • Format: Directory

  • readsFilteringFolder

    • Description: Directory containing filtered sequencing reads from previous processing steps
    • Format: Directory

  • outputDir

    • Description: Output directory for storing UMI assignment results
    • Format: Directory

Outputs

  • umi

    • Description: UMI assignment results including read-to-UMI mappings and binned reads
    • Format: UMI format

  • outputDir

    • Description: Directory containing all output files including alignment results, mapping files, and binned reads organized by sample
    • Format: Directory

References & Resources

  • Tool Documentation: Contact the team for details on Bin_reads.R and Filter_UMIs.R