Skip to content

AdapterRemoval Specifications

Process Details

  • Name: AdapterRemoval
  • Process UUID: 0tflzgs0angwlp78wkrvpmhbxuelfx
  • Process Group: Pre_Processing

Overview

AdapterRemoval is a preprocessing tool that searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data. The process also optionally trims low quality bases from the 3' end of reads following adapter removal, ensuring clean sequencing data for downstream analysis.

This process is implemented in Bash, which utilizes the AdapterRemoval bioinformatics tool for sequence preprocessing.

Key Functionality

  • Adapter Detection and Removal: Identifies and removes adapter sequences from paired-end FASTQ files
  • Quality Trimming: Trims low-quality bases from the 3' end of reads and removes N bases
  • Output Organization: Generates properly paired reads, discarded sequences, and singleton reads in separate output files
  • Performance Optimization: Utilizes multi-threading for efficient processing of large sequencing datasets

Input/Output Specification

Inputs

Required Inputs

  • reads
    • Description: Paired-end sequencing reads requiring adapter removal
    • Format: FASTQ (set of files)

Optional Inputs

  • inputTXTfile
    • Description: Text file containing additional configuration parameters
    • Format: TXT

Outputs

  • reads (paired output 1)

    • Description: Cleaned forward reads with adapters removed and quality trimmed
    • Format: FASTQ (gzip compressed)

  • reads (paired output 2)

    • Description: Cleaned reverse reads with adapters removed and quality trimmed
    • Format: FASTQ (gzip compressed)

  • reads (additional outputs)

    • Description: Discarded sequences and singleton reads from the cleaning process
    • Format: FASTQ (gzip compressed)

Parameters & Settings

This process runs conditionally when the run_adapter_removal parameter is set to "yes". The tool automatically detects adapter sequences and applies quality trimming with multi-threading optimization.

References & Resources

  • Tool Documentation: Contact the team for details on AdapterRemoval configuration and usage
  • Related Papers: Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. https://doi.org/10.1186/s13104-016-1900-2