CROMq is a lossy compression algorithm for quality values.

CROMq can only be used on Linux. CROMq requires fftw3. To download, please check here. The following is an example command of installation.

./configure --enable-threads --enable-shared --enable-sse2
sudo make
sudo make install

The example data that we used is SRR494099. It is a fastq format file, so we need to extract qscores from it. The following example is the simple command to extract qscores from fastq file.

awk NR%4==0 SRR494099.fastq >> SRR494099.qscore

Note that the file must end with .qscore.

Please check here to see how to execute the example code.