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If there are really patents protecting this format, it makes it a complete non-starter for a great deal of work (commercial and academic). Posts like this scare

If there are really patents protecting this format, it makes it a complete non-starter for a great deal of work (commercial and academic). Posts like this scare me. I don't want to devote effort to support a format that I might not be able to use in the future. The only thing that I could think of that might work is putting the patents in some sort of defensive portfolio in much the same way that the Open Invention Network protects Linux. I understand the desire to develop bioinformatics file formats in a more disciplined way than we have done in the past, but this process seems like it may be more of a pain than a benefit. Unfortunately, I couldn't see some of the MPEG-G talks at ISMB this year (other talks were concurrent). Could anyone explain what the benefits of the MPEG-G format is over something like CRAM? I mean, we were already starting to get close to the theoretical minimum in terms of file size. I personally would like to see more support for encryption and robustness (against bitrot) in formats, but this could be done in a very similar way to current formats.

deugtniet 8y ago
I agree, the comparison with CRAM is in the whitepaper of MPEG-G. But the author of the blog has some more recent posts, where he is very skeptical of the claims made with respect to the CRAM format. It's worth the read.
- jkbonfield 8y ago
  Disclaimer - I am the author of the blog. There are no "comparisons with" CRAM in the MPEG-G preprint, only comparison between CRAM and DeeZ, taken from the DeeZ paper. Those comparisons are fair and correct, but obviously were done at the time that paper was written - some 4 years ago. Since then CRAM has moved on (as has deez), but modern CRAM generally beats modern DeeZ if we restrict ourselves to the formats that permit random access (DeeZ has a higher compression non-random access mode). So far there have been no direct data on how well MPEG-G does bar an old slide from a year ago; ISMB talk I think. https://mpeg.chiariglione.org/sites/default/files/events/Mattavelli.pdf https://mpeg.chiariglione.org/sites/default/files/events/Mat... From that we can glean some compression ratios at least. I attempted to compress the same data set with CRAM, but that data set, while public, is in FASTQ format instead of BAM. I asked for author of the talk how he had produced the BAM, but got no response. I tried my best stab at creating something similar, but it's not a satisfactory comparison yet.

deugtniet 8y ago

I agree, the comparison with CRAM is in the whitepaper of MPEG-G. But the author of the blog has some more recent posts, where he is very skeptical of the claims made with respect to the CRAM format. It's worth the read.

jkbonfield 8y ago
Disclaimer - I am the author of the blog. There are no "comparisons with" CRAM in the MPEG-G preprint, only comparison between CRAM and DeeZ, taken from the DeeZ paper. Those comparisons are fair and correct, but obviously were done at the time that paper was written - some 4 years ago. Since then CRAM has moved on (as has deez), but modern CRAM generally beats modern DeeZ if we restrict ourselves to the formats that permit random access (DeeZ has a higher compression non-random access mode). So far there have been no direct data on how well MPEG-G does bar an old slide from a year ago; ISMB talk I think. https://mpeg.chiariglione.org/sites/default/files/events/Mattavelli.pdf https://mpeg.chiariglione.org/sites/default/files/events/Mat... From that we can glean some compression ratios at least. I attempted to compress the same data set with CRAM, but that data set, while public, is in FASTQ format instead of BAM. I asked for author of the talk how he had produced the BAM, but got no response. I tried my best stab at creating something similar, but it's not a satisfactory comparison yet.