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Primers Trimming Specifications

Process Details

  • Name: primersTrimming
  • Process UUID: cdb6269b86ba4db7bca956609be44901
  • Process Group: uminator

Overview

This process handles the trimming of PCR primers and external sequences from polished consensus sequences generated from UMI (Unique Molecular Identifier) data. The process consolidates consensus sequences from multiple UMIs within a sample and optionally removes primer sequences to produce clean, trimmed consensus sequences ready for downstream analysis.

This process is implemented in Bash, which utilizes cutadapt for adapter and primer trimming operations.

Key Functionality

  • Consensus Sequence Consolidation: Locates and concatenates all polished consensus sequences from UMIs within a sample into a single FASTA file
  • Primer Trimming: Removes forward and reverse PCR primers along with their reverse complements from consensus sequences using cutadapt
  • Length Filtering: Applies minimum and maximum length constraints to ensure sequence quality and consistency
  • Conditional Processing: Provides optional primer trimming workflow that can be enabled or disabled based on experimental requirements

Input/Output Specification

Inputs

Required Inputs

  • UMI Data
    • Description: UMI dataset containing consensus sequences from molecular barcoding experiments
    • Format: umi

Outputs

  • Output Directory
    • Description: Directory containing processed consensus sequences, either with or without primer trimming applied
    • Format: directory

Parameters & Settings

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

The process references several configurable parameters including primer sequences (FW_primer, RV_primer), length constraints (minLen, maxLen), and the primer trimming toggle (primersTrimming), though specific parameter annotations are not visible in the provided script header.

References & Resources

  • Tool Documentation: Contact the team for details on cutadapt usage and seqtk sequence manipulation tools