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Download Fastq files from NCBI SRA database

ID: 265FF649-EE80-7CCD-DE95-5893CC981253

The optimal protocol for downloading and exporting fastq files from the NCBI SRA database.

It has two parameters:

  • Accession: which is the SRA record that you want to download. Can be SRAXXXX, GSMXXXX, or SRXXXXX
  • Threads: Number of threads for downloading and compressing

Environment

  • Operation System: Linux/Unix
  • CPU cores: 4
  • Memory: 1GB

Steps

Software Parameter
prefetch {{Accession}}
vdb-validate */*.sra
fasterq-dump */*.sra -e {{Threads||4}}
pigz -p {{Threads||4}} *.fastq
Export