[DAS] DAS and bacterial genomes

Ewan Birney birney at ebi.ac.uk
Thu Aug 19 09:56:49 UTC 2010

Just to repeat :

  I always think this should be easy and then I get educated by Paul:

  I thikn each time one thinks about "just moving it down a  
level" (eg, to strain) there are submitted
cases in which two people have submitted assemblies with the same  
"strain tax id" but actually
clearly arent (eg, there is a big insertion of something). The whole  
thing keeps moving down
a notch.

  The right thing here is to assign tracking idenitifers to assembly  
series independently of
the strain assignments, and track assemblies separately (but obviously  
with relationships)
to strains.

   Paul has met most (?all) of the use cases and understands this  
better than me. I think
we should wait for Paul to weigh in here - it's just always a bit more  
complicated than you
think ;)

On 19 Aug 2010, at 00:10, Andy Jenkinson wrote:

> On 18 Aug 2010, at 20:47, Adam Witney wrote:
>>> As mentioned elsewhere in this thread, the problem of  
>>> distinguishing an individual from its taxon is not limited to  
>>> bacteria. Does  the 1000 genomes project use the assembly as a  
>>> surrogate for isolate/individual?
>> No it's not unique to bacteria, indeed I notice that Plasmodium  
>> vivax is already in the DAS registry, does this not suffer the same  
>> problems? i.e which strain are the coordinates referring to?
> So far a coordinate system always refers to the species or strain  
> identified by its taxonomy ID. As you say, strains DO have their own  
> NCBI taxonomy ID. It may be that this is not the case for a strain  
> that someone wants to annotate, but I have yet to see an actual  
> example. There is the wider question of how to handle individuals  
> though. I can't comment on how 1000 genomes do this as I've only  
> seen these data expressed as variations annotated upon the reference  
> assembly, but my feeling is that if annotations of an individual  
> were needed then it could/would be done using the assembly paradigm  
> as a surrogate.
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