Small Fastq Examples

Contents in this Repo

• generateFastqSample.py: script to generate two shorten fastq examples files from two Paired-end fastq read files.

• ./data/ : folder containing shortened fastq example files

Generating new files

Large FastQ files can be reduced in size using the provided script.

• Download the original fastq to be shortened (into the same folder with this script for example). eg:

  wget https://example.org/full_R1.fastq.gz
  wget https://example.org/full_R2.fastq.gz
  

• Decompress the gunzip files:

• Run the Script to generate two new sample files which preserve 5% of the original reads:

     # generateFastqSample.py PCT_TO_KEEP R1READS_FULL R2READS_FULL 3> R1READS_SMALL 4> R2READS_SMALL
     #
     ./generateFastqSample.py 5  <(gzip -d full_R1.fastq.gz) \
                                 <(gzip -d full_R2.fastq.gz) \
                                3> >(gzip -c short_R1.fastq.gz) \
                                4> >(gzip -c short_R2.fastq.gz)
  
     md5sum short_R1.fastq.gz > short_R1.fastq.gz.md5
     md5sum short_R2.fastq.gz > short_R2.fastq.gz.md5