bio-sra-data

---

name: bio-sra-data description: Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads. tool_type: cli primary_tool: sra-tools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

SRA Data

Download raw sequencing data from the Sequence Read Archive using the SRA toolkit.

Installation

# macOS
brew install sratoolkit

# Ubuntu/Debian
sudo apt install sra-toolkit

# conda (recommended)
conda install -c bioconda sra-tools

# Verify installation
fasterq-dump --version

Core Commands

fasterq-dump - Download FASTQ (Recommended)

Fast, multithreaded FASTQ extraction. Preferred over fastq-dump.

# Download single SRA run as FASTQ
fasterq-dump SRR12345678

# Output: SRR12345678.fastq (single-end)
# Or: SRR12345678_1.fastq, SRR12345678_2.fastq (paired-end)

Key Options:

Option	Description	Example
-O / --outdir	Output directory	-O ./fastq/
-o / --outfile	Output filename	-o sample.fastq
-e / --threads	Number of threads	-e 8
-p / --progress	Show progress bar	-p
-S / --split-files	Split paired reads (default)	-S
-3 / --split-3	Also output unpaired reads	-3
--skip-technical	Skip technical reads	--skip-technical
-t / --temp	Temp directory	-t /tmp
-f / --force	Overwrite existing	-f

# Common usage with options
fasterq-dump SRR12345678 -O ./data/ -e 8 -p --skip-technical

# Force split files (paired-end)
fasterq-dump SRR12345678 -S -O ./data/

prefetch - Download SRA Files First

For large files or unreliable connections, prefetch first, then convert.

# Prefetch SRA file (downloads .sra to ~/ncbi/sra/)
prefetch SRR12345678

# Then convert to FASTQ
fasterq-dump ~/ncbi/sra/SRR12345678.sra

# Or convert in place
fasterq-dump SRR12345678  # Will find prefetched file

Prefetch Options:

Option	Description
-O / --output-directory	Download location
-p / --progress	Show progress
-f / --force	Re-download if exists
--max-size	Max file size (e.g., 50G)
-X / --max-size	Same as above

# Prefetch with size limit
prefetch SRR12345678 --max-size 100G -p

# Prefetch multiple accessions
prefetch SRR12345678 SRR12345679 SRR12345680

# Prefetch from a list file
prefetch --option-file accessions.txt

vdb-validate - Verify Downloads

Check integrity of downloaded SRA files.

# Validate a downloaded file
vdb-validate SRR12345678

# Validate with detailed output
vdb-validate SRR12345678 2>&1

sra-stat - Get Run Statistics

Get information about an SRA run without downloading.

# Basic stats
sra-stat --quick SRR12345678

# Detailed XML output
sra-stat --xml SRR12345678

Configuration

vdb-config - Configure SRA Toolkit

Set up cache location and other settings.

# Interactive configuration
vdb-config -i

# Set cache directory
vdb-config --set /repository/user/main/public/root=/path/to/cache

# Check current configuration
vdb-config --cfg

Cache Location

Default: ~/ncbi/ on Linux/macOS

# Create dedicated cache
mkdir -p /data/sra_cache
vdb-config --set /repository/user/main/public/root=/data/sra_cache

Code Patterns

Download Single Run

#!/bin/bash
SRR="SRR12345678"
OUTDIR="./fastq"

mkdir -p $OUTDIR
fasterq-dump $SRR -O $OUTDIR -e 8 -p

Download Multiple Runs

#!/bin/bash
# From a list of accessions
while read SRR; do
    echo "Downloading $SRR..."
    fasterq-dump $SRR -O ./fastq/ -e 4 -p
done < accessions.txt

Prefetch Then Convert (Large Files)

#!/bin/bash
SRR="SRR12345678"

# Prefetch first (resumable)
prefetch $SRR -p

# Validate
vdb-validate $SRR

# Convert to FASTQ
fasterq-dump $SRR -O ./fastq/ -e 8 -p

# Optionally remove .sra file
rm -f ~/ncbi/sra/${SRR}.sra

Batch Download Script

#!/bin/bash
# download_sra.sh - Download multiple SRA runs

ACCESSIONS="$1"
OUTDIR="${2:-./fastq}"
THREADS="${3:-4}"

mkdir -p $OUTDIR

while read SRR; do
    if [[ -z "$SRR" ]] || [[ "$SRR" == \#* ]]; then
        continue
    fi

    echo "Processing $SRR..."

    # Prefetch
    prefetch $SRR -p -O $OUTDIR

    # Validate
    if ! vdb-validate ${OUTDIR}/${SRR}/${SRR}.sra 2>/dev/null; then
        echo "Validation failed for $SRR, skipping..."
        continue
    fi

    # Convert
    fasterq-dump ${OUTDIR}/${SRR}/${SRR}.sra -O $OUTDIR -e $THREADS -p

    # Cleanup .sra
    rm -rf ${OUTDIR}/${SRR}

    echo "Completed $SRR"
done < "$ACCESSIONS"

Python Wrapper

import subprocess
import os

def download_sra(accession, outdir='.', threads=4, skip_technical=True):
    os.makedirs(outdir, exist_ok=True)

    cmd = ['fasterq-dump', accession, '-O', outdir, '-e', str(threads), '-p']
    if skip_technical:
        cmd.append('--skip-technical')

    result = subprocess.run(cmd, capture_output=True, text=True)
    if result.returncode != 0:
        raise RuntimeError(f"fasterq-dump failed: {result.stderr}")

    return result.stdout

# Download a run
download_sra('SRR12345678', outdir='./data', threads=8)

Find SRA Accessions with Entrez

from Bio import Entrez

Entrez.email = 'your.email@example.com'

def find_sra_runs(term, max_results=100):
    handle = Entrez.esearch(db='sra', term=term, retmax=max_results)
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return []

    handle = Entrez.efetch(db='sra', id=','.join(search['IdList']), rettype='runinfo', retmode='text')
    runinfo = handle.read()
    handle.close()

    # Parse CSV-like output
    runs = []
    for line in runinfo.strip().split('\n')[1:]:
        if line:
            fields = line.split(',')
            if len(fields) > 0:
                runs.append(fields[0])  # First field is Run accession
    return runs

# Find runs for a project
runs = find_sra_runs('PRJNA123456[bioproject]')
print(f"Found {len(runs)} runs")

SRA Accession Types

Prefix	Type	Description
SRR	Run	Individual sequencing run
SRX	Experiment	Experimental design
SRS	Sample	Biological sample
SRP	Project/Study	Research project
PRJNA	BioProject	NCBI BioProject ID
SAMN	BioSample	NCBI BioSample ID

Use Run accessions (SRR*) with fasterq-dump.

Common Errors

Error	Cause	Solution
item not found	Invalid accession	Check accession exists
disk full	Insufficient space	Check temp and output dirs
timeout	Network issues	Use prefetch first
path not found	Bad output path	Create output directory
permission denied	Cache permission	Check vdb-config

Comparison: fasterq-dump vs fastq-dump

Feature	fasterq-dump	fastq-dump
Speed	Fast (multithreaded)	Slow (single-threaded)
Memory	Higher	Lower
Progress	Built-in	None
Recommended	Yes	Legacy only

Always prefer fasterq-dump unless memory constrained.

Decision Tree

Need SRA sequencing data?
├── Know the SRR accession?
│   └── fasterq-dump SRR... -O ./fastq/ -p
├── Large file (>20GB)?
│   └── prefetch first, then fasterq-dump
├── Multiple runs?
│   └── Loop through accessions or use prefetch --option-file
├── Need to find accessions?
│   └── Search SRA database with Entrez
├── Download interrupted?
│   └── prefetch supports resume
└── Verify integrity?
    └── vdb-validate SRR...

Related Skills

• entrez-search - Search SRA database to find accessions
• sequence-io - Read downloaded FASTQ files with Biopython
• sequence-io/paired-end-fastq - Handle paired R1/R2 files
• alignment-files - Align downloaded reads