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Adapter Removal Specifications

Process Details

  • Name: Adapter Removal
  • Process UUID: 20bdc868-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

Performs adapter removal on sequencing reads using either Trimmomatic or Fastx_clipper based on the selected tool. It supports both single-end and paired-end reads, and the adapter sequences can be specified. The process also provides options for setting quality encoding, minimum read length, seed mismatches, palindrome clip threshold, and simple clip threshold.

This process is implemented in Bash, which invokes a Perl script for adapter removal using either Trimmomatic or Fastx_clipper tools.

Key Functionality

  • Flexible Tool Selection: Choose between Trimmomatic and Fastx_clipper for adapter removal based on data type and requirements
  • Paired and Single-End Support: Handles both paired-end and single-end sequencing reads with appropriate processing workflows
  • Customizable Adapter Sequences: Allows specification of single or multiple adapter sequences for removal
  • Quality Control Integration: Provides comprehensive quality filtering with adjustable parameters for read length and matching thresholds

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Sequencing reads in FASTQ format for adapter removal
    • Format: FASTQ

  • Mate

    • Description: Specifies whether the reads are single-end or paired-end
    • Format: Mate designation

Outputs

  • Reads

    • Description: Adapter-trimmed sequencing reads ready for downstream analysis
    • Format: FASTQ

  • Log File

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

Parameters & Settings

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

  • Phred Quality Encoding

    • 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

  • Tool for Adapter Removal

    • Description: Choose adapter removal tool to be used. Note: fastx_clipper is not suitable for paired reads.
    • Available options: trimmomatic (default), fastx_clipper

  • Adapter Sequence

    • Description: Removes 3' Adapter Sequences. You can enter a single sequence or multiple sequences in different lines. Reverse sequences will not be removed. The first 13 bp of Illumina standard adapters(AGATCGGAAGAGC) is set by default.
    • Default value: AGATCGGAAGAGC

  • Minimum Length

    • Description: Specifies the minimum length of reads to be kept
    • Default value: 10

  • Seed Mismatches

    • Description: Specifies the maximum mismatch count which will still allow a full match to be performed
    • Default value: 2

  • Palindrome Clip Threshold

    • Description: Specifies how accurate the match between the two -adapter ligated- reads must be for PE palindrome read alignment.
    • Default value: 30

  • Simple Clip Threshold

    • Description: specifies how accurate the match between any adapter etc. sequence must be against a read
    • Default value: 5

  • Discard Non-Clipped

    • Description: -c: discard_non_clipped sequences (keep only sequences which contained the adapter)
    • Available options: yes (default), no

  • Remove Previous Reads

    • Description: After successful completion of the adapter removal step, previous reads will be removed to save space. However, this might affect resume functionality.
    • Default value: false

References & Resources

  • Tool Documentation: Contact the team for details on the Perl script implementation
  • Related Papers:
  • Bolger, A., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.