[Bioperl-l] What's the best object to store sequence assembly information?

[Elia Stupka]

> Would you happen to know where I can find the thread(s) for this
> topic? I didn't turn up anything useful in the archive searching for
> 'assembly' or 'assemblies'.

Good question, I distinctly remember a long discussion and I've searched a
few folders of mine but can't find it. I think it was definitely not on
the bioperl list but on one of the hackathon related lists, either the
biohackathon list itself or at a later stage on the open-bio list... it
really had to do with the biosql schema to store them....

...a one line summary was that people were debating two views:

1)Provide ability to store assemblies of assemblies in a n-layer
fashion. This would handle for example storing from the initial dna reads,
to contig, to supercontigs, to chromosomes, all within the same
schema. Most flexible but some people felt it was over-complicated for the
guy who "just wants a simple assembly module". Others felt it didn't force
anybody to use it in a multi-layer way.

2)simpler approach, just a 2-layer object with elements and a module to
represent assemblies of these elements, eliminating advantages and
disadvantages of the above

I say you could start by going ahead with what you feel is best, then the
code could be improved,expanded, integrated, but in the meantime you would
kick off the process which we haven't managed to so far ;)


Elia

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