> 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
