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Candidate UMIs Filtering Specifications

Process Details

  • Name: candidateUMIsFiltering
  • Process UUID: 9065f0e0538245f3903bfb666b279cfd
  • Process Group: uminator

Overview

This process filters and processes candidate Unique Molecular Identifiers (UMIs) to create high-quality UMI databases for molecular barcoding applications. The process performs pattern matching, dereplication, clustering, and validation steps to ensure only reliable UMIs are retained for downstream analysis.

This process is implemented in Bash, which utilizes multiple bioinformatics tools including vsearch, bwa, samtools, and seqtk for UMI processing and validation.

Key Functionality

  • Pattern-based Filtering: Filters candidate UMIs based on specified sequence patterns to ensure structural integrity
  • Dereplication and Clustering: Removes duplicate sequences and clusters similar UMIs to create a non-redundant database
  • Support Validation: Retains only UMIs that are supported by at least 3 candidate sequences to ensure reliability
  • Dual-part UMI Processing: Splits UMI sequences into two parts and generates both forward and reverse complement orientations

Input/Output Specification

Inputs

Required Inputs

  • outputDir
    • Description: Directory containing candidate UMI extraction results from previous processing steps
    • Format: Directory

Outputs

  • outputDir
    • Description: Directory containing filtered and processed UMI databases, including separate files for UMI part 1 and part 2 in forward and reverse complement orientations
    • Format: Directory

Parameters & Settings

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

  • UMI Pattern

    • Description: Regular expression pattern for filtering candidate UMIs based on sequence structure
    • Default value: Process-specific pattern

  • UMI Length

    • Description: Length of individual UMI sequences for processing and trimming operations
    • Default value: Process-specific length

  • UMI Cluster Identity

    • Description: Identity threshold for clustering dereplicated UMIs to create the final database
    • Default value: Process-specific identity threshold

  • Maximum Differences

    • Description: Maximum number of differences allowed during UMI alignment for validation
    • Default value: Process-specific difference threshold

References & Resources

  • Tool Documentation: Contact the team for details on the UMI filtering pipeline implementation
  • Related Papers:
  • Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584. DOI: 10.7717/peerj.2584
  • Li H, Durbin R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-60. DOI: 10.1093/bioinformatics/btp324