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Scrub Fastq Captions Specifications

Process Details

  • Name: scrub_fastq_captions
  • Process UUID: f9313afbeocqryh462n1q9piae3pty
  • Process Group: Binning

Overview

This process cleans and processes FASTQ files to remove or alter specific captions for MetaPhlAn4 analysis. It prepares sequencing data by standardizing read headers and formatting to ensure compatibility with downstream taxonomic profiling workflows.

This process is implemented in Bash, which invokes a Python script for FASTQ caption processing.

Key Functionality

  • Caption Scrubbing: Removes or modifies problematic headers and captions in FASTQ files that may interfere with MetaPhlAn4 processing
  • Batch Processing: Processes multiple FASTQ files in parallel to improve efficiency
  • Format Standardization: Ensures FASTQ files conform to expected formatting standards for taxonomic analysis
  • MetaPhlAn4 Preparation: Specifically optimizes files for compatibility with MetaPhlAn4 taxonomic profiling pipeline

Input/Output Specification

Inputs

Required Inputs

  • Reads

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

  • Mate

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

Outputs

  • Fastq Reads
    • Description: Cleaned FASTQ files with processed captions, ready for MetaPhlAn4 analysis
    • Format: FASTQ

Parameters & Settings

This process runs automatically when enabled and does not require user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on scrub_fastq_captions.py
  • Related Papers: Blanco-Míguez, A., Beghini, F., Cumbo, F., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology, 41(11), 1633-1644.