4 ms·

Yeah that's exactly the issue. A lot of tools are written once and rarely updated, they're considered "done". And they only support gz out of the box because th

• jltsiren 4y ago
  I think the tools people actually use are rarely that old. Almost all new tools support gzip by default, because almost all public data is gzip-compressed. Developers often don't bother adding zstd support, because there is little zstd-compressed data around. Because the labs developing new tools are rarely the ones that have to store petabytes of data, they don't benefit from zstd directly. And once the active development is over, most tools receive only minimal support, because nobody wants to pay for maintaining the long tail of average tools. Also, zstd is the latest reason why gzip is still widely used. Every time someone releases a new general-purpose data compressor that becomes popular, gzip gains a few more years. Because there have been too many gzip replacements over the years, none of them has managed to become popular enough to actually replace gzip before the attention moves to the next state-of-the art compressor. If people agreed this time that zstd is what everyone will be using for the next 20 years, bioinformatics would probably move to it in a few years.
• asdff 4y ago
  But that's hardly an issue, since you can just add the new compression tool to your pipeline before and after the older tool. Many tools don't even support gzip because they assume the user will be piping in uncompressed data from zcat anyway.