[Bioperl-l] Simple sequence assemblies

[Elia Stupka]

> 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 ...

Well that is exactly the direction I want to take. Basically, let's put it
this way, we have created the bioperl-pipeline, and the core is reaching
stability, so now we just need to decide which parts (having done basics
like blast,etc) we want to plug in, and make sure they work well within
the pipeline. There is a wealth of things we could look into, so the
approach I am taking is to link our development with a few
real-world-needed pipelines that we meet by collaborating with wet labs.

And the top requests at the moment are for going from
traces->sequences->simple annotation as well as
ests->clusters->sequences->simple annotation

For ESTs we are working with SANBI folks to "bioperlise" and parralelise
STACK, so that it could be run as part of the pipeline. For traces and
mini-assemblies I was thinking the classic phrap (which is also used
within STACK at some point) but if other people have better ideas, please
do suggest.

On the side we would also like to have simple viewing via a modified
GMOD/Bio-Graphics system, which we already use internally to look at
analysis we do that is not ensembl based.

We are presenting the pipeline at BOSC, so we are aiming by then to have
some successful example designs running on the cluster,etc. (we are
already using it, but for simple pipelines only) Also we are going to
start using it to populate our ensembl database for analysis that we have
developed since we started using the bioperl pipeline (that's the neat
thing about bioperl pipe, that it can write to whatever you want...)

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

No, this one I am not giving in, yet ;)

Elia

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