getFastq

A BASH script for downloading and extracting Fastq files from SRA files from SRA without needing the SRA-toolkit. Avoiding prefetch may be convenient for your workflow as it was for mine.

Features

• Use of parallel-fastq-dump, vastly speeding up SRA-Fastq extraction times.
• Attempts to download SRA files with ascp first before getting the https:// url for the SRR using Edirect.
• Attempts to download accessions twice in case of error.
• Pass-through options for parallel-fastq-dump
  • -t : threads
  • -d : temporary directory for parallel-fastq-dump
• Pass-through options for ascp
  • -b : bandwidth in the format of m. E.g. 900m

Dependencies

1. Ability to execute BASH scripts.
2. Aspera CLI installed in /home/${USER}/.aspera (The default).
3. Curl
4. Edirect on $PATH.
5. parallel-fastq-dump on $PATH.

Instructions

• The script reads accessions from stdin, removing quotations and ignoring strings that do not start with SRR.
  • Pipe inputs using $./getFastq.sh -t 30 < accessions.txt
  • Pipe inputs using $cat accessions.txt | ./getFastq.sh -t 30