Apart from tuning up the compression you may gain a lot by clustering reads in FASTQ files using clumpify from BBMap: https://jgi.doe.gov/data-and-tools/softwa

Apart from tuning up the compression you may gain a lot by clustering reads in FASTQ files using clumpify from BBMap: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb... You may also filter out duplicates and depending on what you do correct base errors or get rid of low complexity reads.