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Filter Low Qual Specifications

Process Details

  • Name: filter_low_qual
  • Process UUID: gzesgvtyoe6cedlu3b59p4wwfido2z
  • Process Group: Pre_Processing

Overview

This process filters low quality sequences from paired-end FASTQ files using fastp, a fast all-in-one preprocessing tool for FASTQ files. The process removes reads with low quality scores and optionally performs deduplication to improve downstream analysis quality.

This process is implemented in Bash, which invokes fastp for quality filtering and preprocessing.

Key Functionality

  • Quality Filtering: Removes reads with quality scores below the specified threshold (default Q30)
  • Deduplication: Optionally removes duplicate reads/pairs to reduce redundancy
  • Report Generation: Creates detailed JSON and HTML reports of the filtering process
  • Paired-end Support: Maintains proper pairing of reads during filtering

Input/Output Specification

Inputs

Required Inputs

  • reads

    • Description: Paired-end FASTQ files containing raw sequencing reads
    • Format: FASTQ (compressed or uncompressed)

  • mate

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

Outputs

  • reads

    • Description: Quality-filtered paired-end FASTQ files
    • Format: FASTQ (gzip compressed)

  • outputJson

    • Description: JSON report containing detailed filtering statistics and quality metrics
    • Format: JSON

  • logOut

    • Description: Log file containing process execution details and summary statistics
    • Format: OUT

Parameters & Settings

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

  • The quality value that a base is qualified

    • Description: The quality value that a base is qualified. Default 30 means phred quality >=Q30 is qualified.
    • Default value: 30

  • Enable deduplication to drop the duplicated reads/pairs

    • Description: Enable deduplication to drop the duplicated reads/pairs?
    • Available options: false (default), true

References & Resources

  • Tool Documentation: Contact the team for details on fastp
  • Related Papers: Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884-i890. https://doi.org/10.1093/bioinformatics/bty560