The code is here:
Documentation can be found here:
We just released v0.7, which is not a long term support yet but stable enough to try it out.
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I am the developer of CRAM and can answer any questions about it.
The code is here:
Documentation can be found here:
We just released v0.7, which is not a long term support yet but stable enough to try it out. -
Supporting all the tags is expected in CRAM 0.7 due soon, see e.g.Originally posted by lh3 View Post
I heard at a recent seminar that the CRAM team are looking at doing a mini-assembly of the unmapped reads in order to generate dummy reference sequences which can then be used for reference based compression. If I understood correctly this might be transparent to the user.Originally posted by lh3 View Post
Also at the same seminar we were told CRAM has several modes of quality compression, one of which is simply reducing the resolution.Originally posted by lh3 View PostLeave a comment:
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Yes, cram has a great potential. It may ultimately replace BAM (if cram does not do that, there will be a binary format to achieve sooner or later). Nonetheless, cram may not replace BAM right now. It does not (at least did not) support all the tags. I do not know the progress on compressing unmapped reads. Furthermore, I am concerned with the compression model. I also think lossy compression is the way to go, but this should be done by reducing the resolution of quality, instead of by selectively dropping all the quality information.Leave a comment:
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I've heard Sanger is considering it, perhaps even this year if CRAM continues to mature rapidly.Leave a comment:
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Cram
Hi Guys,
Anyone already thought about deploying CRAM for archiving alignment data, rather than BAM?
Our Illumina representative told us they want to switch to that format...
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Whole Transcriptome RNA-seq
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