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From Evert Lammerts <Evert.Lamme...@sara.nl>
Subject RE: Hadoop for Bioinformatics
Date Thu, 31 Mar 2011 07:15:41 GMT
> The short answer is yes!  At CRS4 we are working on this very problem.
>
> We have implemented a Hadoop-based workflow to perform short read
> alignment to
> support DNA sequencing activities in our lab.  Its alignment operation
> is
> based on (and therefore equivalent to) BWA.  We have written a paper
> about it
> which will appear in the coming months, and we are working on an open
> source
> release, but alas we haven't completed that task yet.
>
> We have also implemented a Hadoop-based distributed blast alignment
> program,
> in case you're working with long fragments.  It's currently being used
> by our
> collaborators to align viral DNA segments.
>
>
> In either case, if you're interested we can let you have an advance
> release of
> either program so you can try them out.

Hi Luca,

Could you send me an advanced release of your software? I work for the Dutch national center
for scientific computing, and I will give a workshop on Hadoop to BioInformatics on a large
BI conference (http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2011/). Lots
of people there work with BWA and BLAST type applications (among others in the BBMRI project,
which I think CRS4 is involved in as well). So BWA on Hadoop could be a great case study.

Let me know!
Cheers,
Evert

>
>
> --
> Luca Pireddu
> CRS4 - Distributed Computing Group
> Loc. Pixina Manna Edificio 1
> Pula 09010 (CA), Italy
> Tel:  +39 0709250452

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