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Trimmer Specifications

Process Details

  • Name: Trimmer
  • Process UUID: 20bdcaa2-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

The Trimmer process performs quality-based trimming of sequencing reads using the fastx_trimmer tool. This process allows for flexible trimming of both single-end and paired-end reads by removing specified lengths from the 5' and 3' ends of sequences. It automatically detects read length and applies trimming parameters accordingly, making it suitable for preprocessing raw sequencing data before downstream analysis.

This process is implemented in Bash, which invokes a Perl script for read length detection and trimming parameter calculation.

Key Functionality

  • Flexible Read Trimming: Supports trimming from both 5' and 3' ends with customizable lengths for single-end and paired-end reads
  • Automatic Length Detection: Analyzes the first 100 reads to determine sequence length before applying trimming parameters
  • Quality Encoding Support: Handles both Phred+33 and Phred+64 quality score encodings for compatibility with different sequencing platforms
  • Space Management: Optional removal of input files after successful trimming to conserve storage space

Input/Output Specification

Inputs

Required Inputs

  • reads

    • Description: Input sequencing reads in FASTQ format (single-end or paired-end)
    • Format: fastq

  • mate

    • Description: Specifies whether the input consists of single-end or paired-end reads
    • Format: mate

Outputs

  • reads

    • Description: Trimmed sequencing reads in FASTQ format
    • Format: fastq

  • log_file

    • Description: Log file containing trimming statistics and process information
    • 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

  • Trimming Length from 5' End

    • Description: Trimming length from 5' end
    • Default value: 0

  • Trimming Length from 3' End

    • Description: Trimming length from 3' end
    • Default value: 0

  • Trimming Length from 5' End of R1 Reads

    • Description: Trimming length from 5' end of R1 reads
    • Default value: 0

  • Trimming Length from 3' End of R1 Reads

    • Description: Trimming length from 3' end of R1 reads
    • Default value: 0

  • Trimming Length from 5' End of R2 Reads

    • Description: Trimming length from 5' end of R2 reads
    • Default value: 0

  • Trimming Length from 3' End of R2 Reads

    • Description: Trimming length from 3' end of R2 reads
    • Default value: 0

  • Remove Previous Reads

    • Description: After successful completion of the trimming 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 trimming script