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vasi / pixz

Parallel, indexed xz compressor
BSD 2-Clause "Simplified" License
712 stars 61 forks source link

the oldest indexing compressor ? #119

Open maximilianh opened 4 months ago

maximilianh commented 4 months ago

Hi Dave,

about the "similar tools" section on this page, you may want to add "pgzip" ? https://github.com/vasi/pixz

in genomics, the indexing compressor pgzip has been used for around 15 years. Millions of files on the internet use it, it allows streaming of sequencing reads and variant files in vcf.gz so you can load only a part of the file over HTTP, only the one for the chromosome location that you're currently viewing. Browsers like UCSC, Ensembl or NCBI support this format, as well as standalone apps like IGV. Of the indexing compressors, pgzip may be the one with the largest adoption and oldest history?

vasi commented 4 months ago

There's a few things called "pgzip" out there if I google. Which one did you have in mind?

maximilianh commented 3 months ago

Sorry bgzip! http://www.htslib.org/doc/bgzip.html

On Sat, Jul 6, 2024 at 07:11 Dave Vasilevsky @.***> wrote:

There's a few things called "pgzip" out there if I google. Which one did you have in mind?

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