Using larger-than-default window sizes has the drawback of requiring that the same --long=xx argument be passed during decompression reducing compatibility somewhat.

Took me a while to realize that Grace Blackwell refers to a person and not an Nvidia chip :)

I’ve worked with large genomic datasets on my own dime, and the default formats show their limits quickly. With FASTA, the first step for me is usually conversion: unzip headers from sequences, store them in Arrow-like tapes for CPU/GPU processing, and persist as Parquet when needed. It’s straightforward, but surprisingly underused in bioinformatics — most pipelines stick to plain text even when modern data tooling would make things much easier :(

For me it was an increasing number (think of unix timestamps in a data logger that stores one entry per second, so you are just counting up until there's a gap in your data), in the article it's a fixed value every 60 bytes

Of course, our brains are exceedingly good at finding patterns (to the point where we often find phantom ones). I was just expecting some basic checks like "does it make sense to store the difference instead of the absolute value for some of these bytes here". Seeing as the difference is 0 between every 60th byte in the submitted article, that should fix both our issues

Bzip2 performed much better for me but it's also incredibly slow. If it were only the compressor, that might be fine for many applications, but also decompressing is an exercise in patience so I've moved to Zstandard at the standard thing to use

    > title
    bases with optional newlines
    > title
    bases with optional newlines
    ...

It makes a lot of sense that this would work: bacteria have many subsequences in common, but if you insert non-semantic newlines at effectively random offsets then compression tools will not be able to use the repetition effectively.