If you have re-sequencing data of model species (which applies to >80% of generated sequencing data), the storage issue is often solved using CRAM/BAM formats.

If you have re-sequencing data of model species (which applies to >80% of generated sequencing data), the storage issue is often solved using CRAM/BAM formats. The FASTQ can be reconstructed if unmapped reads are stored in the file. More general (pre-alignment) sequence compression methods never really took of (e.g. https://github.com/BEETL/BEETL https://github.com/BEETL/BEETL). Probably because it helps so much to have common format that most workflows can start with. Here, the replacement of gzip with zstd would be a lower hanging fruit.