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Fastq Dump Specifications

Process Details

  • Name: fastq_dump
  • Process UUID: 874dd8wouvuzpxtv9i4lpr4sfw01jz
  • Process Group: Misc.

Overview

This process downloads FASTQ files from the NCBI Sequence Read Archive (SRA) using the fastq-dump tool from the SRA Toolkit. It converts SRA format files to standard FASTQ format, which is essential for downstream sequencing data analysis workflows.

This process is implemented in Python, which configures and executes the fastq-dump command-line tool for SRA data retrieval.

Key Functionality

  • SRA Data Download: Downloads sequencing data from NCBI SRA database using SRR accession numbers
  • Format Conversion: Converts proprietary SRA format to standard FASTQ format with gzip compression
  • Flexible Output Handling: Supports both single-end and paired-end sequencing data with automatic file naming
  • Robust Error Handling: Implements retry mechanism with up to 3 attempts for failed downloads
  • Technical Read Filtering: Optional filtering of technical reads during the conversion process

Input/Output Specification

Inputs

Required Inputs

  • Input Tuple
    • Description: CSV file containing SRR accession numbers and corresponding file names for batch processing
    • Format: CSV

Outputs

  • Reads
    • Description: Downloaded and converted FASTQ files, compressed with gzip. Output format depends on sequencing type (single-end produces .fastq.gz, paired-end produces _R1.fastq.gz and _R2.fastq.gz)
    • Format: FASTQ

Parameters & Settings

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

  • Split Mode

    • Description: Controls how paired-end reads are split into separate files
    • Default value: Determined by params.split_mode configuration

  • Skip Technical Reads

    • Description: Whether to exclude technical reads from the output
    • Available options: Yes (default), No

References & Resources

  • Tool Documentation: Contact the team for details on the fastq-dump implementation
  • Related Papers: Leinonen, R., Sugawara, H., & Shumway, M. (2011). The sequence read archive. Nucleic acids research, 39(suppl_1), D19-D21.