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UMI extract Specifications

Process Details

  • Name: UMIextract
  • Process UUID: 20bdb968-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

UMIextract is a bioinformatics process designed to extract Unique Molecular Identifier (UMI) sequences from FASTQ files using specified patterns and incorporate the UMI sequences into read headers. This process is essential for UMI-based sequencing protocols where molecular barcodes are used to identify and quantify individual molecules, enabling more accurate quantification and duplicate removal in downstream analyses.

This process is implemented in Bash, which invokes UMI-tools for UMI extraction and processing.

Key Functionality

  • UMI Pattern Extraction: Extracts UMI sequences from reads using user-defined regex patterns for both single-end and paired-end sequencing data
  • Quality Filtering: Applies quality thresholds to UMI sequences to ensure only high-quality barcodes are retained
  • Header Integration: Incorporates extracted UMI sequences into FASTQ read headers for downstream processing
  • Duplicate Removal: Optionally removes duplicate reads based on UMI sequences to reduce PCR amplification bias

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: FASTQ files containing sequencing reads with UMI sequences
    • Format: FASTQ

  • Mate

    • Description: Specification of whether reads are single-end or paired-end
    • Format: mate (single/pair designation)

Outputs

  • Reads

    • Description: Processed FASTQ files with UMI sequences extracted and incorporated into read headers
    • Format: FASTQ

  • Log File

    • Description: Processing log containing extraction statistics and quality metrics
    • Format: LOG

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Single or Paired End Reads

    • Description: Specification of read type for appropriate processing
    • Available options: single (default), pair

  • Barcode Pattern 1

    • Description: Pattern for UMI extract. Examples: https://www.viafoundry.com/vpipe/index.php?np=1&id=41
    • Default value: ""

  • Barcode Pattern 2

    • Description: Secondary barcode pattern for paired-end reads
    • Default value: ""

  • UMI Quality Filter Threshold

    • Description: Quality (phred quality score) cutoff for UMI. Default is 13, that is UMI with qualities >= 13 will be kept.
    • Default value: 13

  • Phred

    • Description: Specifies the fastq quality encoding. Default is 33 which is now almost universally used, and 64 which is used in some older Illumina data
    • Available options: 33 (default), 64

  • Remove Duplicates Based on UMI

    • Description: Removes duplicate reads by checking UMI.
    • Default value: false

References & Resources

  • Tool Documentation: Contact the team for details on UMI-tools usage and pattern specifications
  • Related Papers: Smith, T., Heger, A., & Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Research, 27(3), 491-499.