sraPrefetcher

Overview

Prefetch SRA data from NCBI using the SRA Toolkit. Supports both public and controlled-access (dbGaP) data.

sraPrefetcher.sh

sbatch --job-name=[jobName] ~/atelier/bin/sraPrefetcher.sh -l [accessionList] [options]

Option	Description
`-l [accessionList]`	Text file containing SRA accession IDs (one ID per line)
`-o [outputDir]`	Output directory for prefetched files (default: current directory)
`-n [ngcFile]`	Path to .ngc file for dbGaP controlled-access data
`-m [maxSize]`	Maximum download size (default: 500G)
`-r`	Resume incomplete downloads
`-d`	Dry run
`-v`	Verbose output with debug logging
`-h`	Display help message

Basic public data prefetch

sbatch --job-name=sra-test ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt

Download to specific directory

sbatch --job-name=sra-download ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt \
    -o /data/sra/

Controlled-access data with dbGaP key

sbatch --job-name=sra-dbgap ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt \
    -n prj_1234.ngc

Custom size and resume

sbatch --job-name=sra-large ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt \
    -m 1T \
    -r

Verbose/debug mode

sbatch --job-name=sra-verbose ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt \
    -v

Dry run preview

sbatch --job-name=sra-preview ~/atelier/bin/sraPrefetcher.sh \
    -l accessions.txt \
    -d