Hello Daniel,
That's a very interesting project(DNA sequencing), I would be happy to have the opportunity to work on it.
When you say "the algorithms I have used are sub-optimal they need to be improved" you are referring to the mathematical underlying, the C code speed or both? For the C code speed-up one may take advantage of multiple cores, by paralelizing it (with MPI or MP). If a really large number of processors is needed, one may use the Amazon HPC service (see for instance ht t p:/ /arstechnica.c om/information-technology/2013/11/18-hours-33k-and-156314-cores-amazon-cloud-hpc-hits-a-petaflop/ ) - (please remove spaces)
For alternative algorithms one may look at "published literature", as you suggested.
This is what I do actually: put scientific algorithms found in research articles into code,on one hand, and code optimization on the other hand. Plese take a look at my short video exhibiting this, ww w.youtube.c om/watch?v=nfjHY9GdI2g
In that particular project I implemented several robust non-linear regression algorithms. I am a mathematician,by the way.
What is to be done with the data you provided, what is the difficulty in dealing with it?
Thank you and I look forward to hearing from you. Adrian