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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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vbz compression compatibility with guppy_basecaller #64

Closed nick-youngblut closed 2 years ago

nick-youngblut commented 2 years ago

The README docs don't seem to state whether guppy_basecaller can read vbz-compressed files, and if yes, what the difference in file reading speed is versus uncompressed fast5 files.

fbrennen commented 2 years ago

Hi @nick-youngblut -- we haven't stated this because all vaguely-recent versions of guppy are capable of reading any fast5 file produced by ont_fast5_api (including vbz-compressed ones).

Vbz benchmarks are generally found in the vbz_compression project, though I do note there is not actually a speed comparison of reading uncompressed vs vbz there. In basic use the speed of fast5 file reading is insignificant compared to the time it takes to basecall those reads, which is why we haven't mentioned it. It can matter for more advanced users running guppy_basecall_server, and there are special tools to address that which are covered in the guppy documentation.

Is there a specific issue you're having?

nick-youngblut commented 2 years ago

Thanks @fbrennen! I'm not running into a specific issue. I just am trying to evaluate options for storing and processing Nanopore data, and it wasn't fully clear what the good/bad aspects of vbz compression were.