[Bioperl-l] Simple sequence assemblies

[Elia Stupka]

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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