prefetch and fasterq-dump #

• These tools are very helpful for downloading raw sequencing reads. Here is how I use them:

  1prefetch -p --max-size 250g \
  2--output-directory /workdir/raw_reads/prefetch \
  3SRR2105768
  4
  5fasterq-dump -e 30 \
  6/workdir/raw_reads/prefetch/SRR2105768/SRR2105768.sra \
  7--outdir /workdir/raw_reads
  

• Make sure to adjust the number of threads with -e.
• I work on machines with low root disk space. Therefore I configured SRA Toolkit to not use the default directories within the home directory for temporary files.