fasterq-dump

name	fasterq-dump
description	Use when extracting FASTQ or FASTA files from NCBI SRA run accessions, especially after staging runs locally with prefetch.
disable-model-invocation	true
user-invocable	true

fasterq-dump

Quick Start

• Command: fasterq-dump
• Local executable: Not installed in this workspace
• Full reference: See references/help.md

When To Use This Tool

• Convert an SRA run accession into FASTQ files for alignment, QC, or assembly.
• Prefer this over legacy fastq-dump for large public SRA runs when you have enough scratch space.
• Use it after prefetch when you want conversion to read from a local accession cache instead of streaming from NCBI.

Common Patterns

# 1) Convert a run accession into paired FASTQ files in a dedicated output directory
fasterq-dump SRR000001 --split-files -e 8 -O fastq -t /scratch

# 2) Best practice for larger runs: prefetch first, then convert from the local accession directory
prefetch SRR000001
fasterq-dump ~/ncbi/public/sra/SRR000001 --split-files -e 8 -O fastq -t /scratch

# 3) Stream a single split-spot FASTQ to stdout for ad hoc processing
fasterq-dump SRR000001 --split-spot -Z | gzip > SRR000001.fastq.gz

Recommended Workflow

1. Resolve the exact run accession and, for large jobs, download it locally with prefetch first.
2. Set an output directory with -O and a roomy scratch directory with -t, ideally on different filesystems.
3. Pick the output mode deliberately: --split-files for paired-end files, --split-spot for a single stream, or --fasta-unsorted when FASTA is enough.
4. Validate the resulting FASTQ filenames and sizes, then compress afterward with gzip or pigz if needed.

Guardrails

• This tool is not installed locally right now, so these patterns are based on upstream SRA Toolkit behavior rather than a live binary in this workspace.
• fasterq-dump takes one accession at a time and writes output into the current directory unless -O is supplied.
• The tool also creates a temporary fasterq.tmp.* directory and can require very large scratch space, with worst-case usage on the order of multiple times the final FASTQ size.
• --stdout does not work with the default split-3 behavior or with --split-files; use --split-spot or another single-stream mode when redirecting output.
• There is no built-in gzip output mode; compress files explicitly after conversion.