I need a a software for genome assembly based on an algorithm of mine. In genome assembly the software is given millions of strings (reads) and merges two strings based on some detected overlap between them. For example:
AAGTTAAATGAGA and GTTCCCAAGTTAA will merge into:
GTTCCCAAGTTAAAAGTTAAATGAGA because AAGTTAA is a an overlapping string between them. So basically, for every set of strings with overlap between the you are looking for "the shortest common superstring" that both of them are sub-strings of it.
I have some variation to this process, which I'll explain in detail later.
I need the software to work in parallel on CUDA. The amount of data here is massive. Millions of strings, each of length 40~150. There are some known algorithms how to quickly construct overlap graphs (look for ABySS assembler for example) using hash tables, prefix graph etc.
There should be at least a basic GUI to load a file, watch the progress and get statistics about the output.
THE MAIN TASK HERE IS: The algorithm must be efficient time-wise. It should be able to process hundreds of millions of string in few hours (some algorithms for genome assembly, like SOAPdenovo are even faster than that, though they are using different approach other than aimple overlap detection [de-bruijn graph]). It is very simple to write the software, but it is not that simple to write it efficiently.
Bid only if you are willing to read about the subject (the biological background). I will provide you with a list of many similar software some of them are open-sourced so you can make use of.
I am myself a programmer and I have the code written in Perl and in Matlab (not very efficiently). It is not good enough to help you, but just to let you know that I will be able to understand your questions and to answer them.
20 freelance font une offre moyenne de $1270 pour ce travail
Hello, I am an expert on C/C++ and I am very experienced in optimizing algorithms. Quality job guaranteed.
Very interested to work on this project. Available to start immediately and finish as soon as possible. Please contact in PMB to discuss details if you are interested in the offer. Best Regards, Zeke
Here is an excellent example of the using CUDA technology in bioinformatics: CUDASW ([url removed, login to view])
i have the experince to finish your project as you requist using OpenMP or MPI or even OpenCL to get the best performanc please check your pmb
Greetings! I am very interested in your project and would gladly do the work you need doing. Check your inbox for details. Sincerely
I have been reading a lot about computational molecular biology for my Msc research for the past year. Sequence alignment, multiple sequence alignment, protein folding (homology based, Ab-initio based), motif identific Plus
Hi. My name is Shad Nygren. I am interested to bid on your project. I have Master's in Computer Science and for my thesis I did some similar sequence alignment and wrote code in C++ [url removed, login to view] Plus
Dear Sir, With my previous GPU (CUDA) development experience for Multiple sequence alignment and levenstein and needleman wunsch algos I am sure to tackle your software very efficiently . Please check you personal e Plus
Hello, I'm happy to bid for this project as it seems to perfectly match the combination of my skills: I have both an MS degree in genetics and 20 years of experience in software development. I'm about to use C/C++ fo Plus
hi, i can propose here 2 solution : 1 - creating whole aplication from begining using CUDA all in c++ ( this option will take a 7-14 days ) 2 - rebulding your Matlab aplication so it will use CUDA and speed up Plus