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Mask Reads Specifications

Process Details

  • Name: mask reads
  • Process UUID: f931tjn02saaqs7omihhj92ks2ewhm
  • Process Group: Binning

Overview

This process masks low-quality regions in input FASTQ files using BBMask from the BBMap suite. It identifies and masks bases that fall below quality thresholds, helping to improve downstream analysis by reducing the impact of sequencing errors and low-confidence base calls.

This process is implemented in Bash, which utilizes the BBMask tool from the BBMap bioinformatics package.

Key Functionality

  • Quality-based masking: Identifies and masks low-quality bases in FASTQ sequences
  • Parallel processing: Processes multiple FASTQ files simultaneously using available CPU threads
  • Batch operation: Handles sets of FASTQ files efficiently with automated file naming

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Set of FASTQ files containing sequencing reads to be masked
    • Format: FASTQ (.fastq.gz)

  • Mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: Mate file

Outputs

  • Reads
    • Description: Masked FASTQ files with low-quality regions replaced by N characters
    • Format: FASTQ (.fastq.gz)

Parameters & Settings

This process uses default BBMask parameters and does not expose user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on BBMask from the BBMap suite
  • Related Papers: Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner. Lawrence Berkeley National Laboratory. Available at: https://sourceforge.net/projects/bbmap/