npm

sratoolkit

Tools for downloading and processing NCBI Sequence Read Archive data

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About

Data tools for INSDC Sequence Read Archive

Commands

fastq-dumpfasterq-dumpprefetchvdb-validatesam-dumpsra-stat

Examples

Download a SRA dataset by accession number$ prefetch SRR12345678
Convert SRA file to FASTQ format$ fasterq-dump SRR12345678.sra -o output.fastq
Validate integrity of a SRA file$ vdb-validate SRR12345678.sra