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Would seekable zstd speed up seqkit? #496

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fdecarpentier opened this issue Nov 22, 2024 · 0 comments
Open

Would seekable zstd speed up seqkit? #496

fdecarpentier opened this issue Nov 22, 2024 · 0 comments

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@fdecarpentier
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I don't really know how seqkit works with compressed fasta files. But I ran into this seekable zstd fasta format developed for the amazing Logan project.
Here is the paper : https://www.biorxiv.org/content/10.1101/2024.07.30.605881v1
And the code : https://github.com/asl/f2sz

The command help also gives more information :

f2sz: FASTA 2 seekable zstd.
It compress a file into a seekable zstd, splitting the file into multiple frames.
The compressed archive can be decompressed with any Zstandard tool, including zstd.

To take advantage of seeking see the following projects:
	C/C++ library:  https://github.com/martinellimarco/libzstd-seek
	Python library: https://github.com/martinellimarco/indexed_zstd

I hope this comment is relevant to seqkit.
Cheers!

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