In modern genomics, you are seeing more and more use of BAMs (Binary versions of SAM files which themselves are Sequence Alignment Files) even for unaligned data that FASTQ was normally used for. Not only are they smaller in size, but they themselves have a compressed format called CRAM which can use lossy or lossless compression depending on the use case.

Interestingly almost all of the petabyte scale and beyond processing of genomes (whole or exome) is done on the JVM as the library and toolkit ecosystem is extremely mature and it is significantly more performant than just scripting things in Perl. Having access to the big data ecosystem that runs on the JVM is also another reason why languages like Java and Scala are found in the high performance areas of genomics.