[Bioperl-l] Simple sequence assemblies

[Hilmar Lapp]

What would be really useful is to have a generic assembly framework where you can plug your vector masking and alignment program (wrapped as modules) as you see fit ...

Also, a way to extract high-quality discrepancies from the aligment ...

<heresy>And the whole thing in Java! (hi Dave)</heresy> ;))

Sorry, I don't want to distract you :-)

Jokes aside, any plans in your shop regarding the above? 

	-hilmar

> -----Original Message-----
> From: Elia Stupka [mailto:elia@fugu-sg.org]
> Sent: Wednesday, June 12, 2002 1:31 AM
> To: Bioperl
> Subject: [Bioperl-l] Simple sequence assemblies
> 
> 
> Hello folks,
> 
> (as usual I might have missed some of the debates on this)
> 
> I am faced by more and more small-medium places that would 
> like an easy
> way to take reads from their labs (we are not talking genomes 
> here) and
> pipe them through a simple pipeline to get small assembled 
> sequences out.
> 
> I know we have a wrapper for consed, but we don't really have 
> wrappers for
> phrap and phred, right? Also the CrossMatch wrapper in 
> Ensembl never made
> its way into bioperl did it?
> 
> Just want to understand what is done and what is outstanding 
> before we go
> ahead and code it. Also any opinions by people that do these sort of
> mini-assemblies would be more than welcome as to how best to 
> tackle this
> problem in a simple manner.
> 
> Elia
> 
> -- 
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