Random-Permutations-Based Aligner (Prototype)
This is a basic example implementation of a Random-Permutations-Based Aligner/Mapper (RPA P3 / RPM P3).
Download page: RPA_P3.
Please read the readme.txt file and try to run the examples.
This prototype includes several improvements to the basic algorithm. For example, “shortcuts” are used to accelerate the binary search. However, this is a SIMPLIFIED PROTOTYPE.
For the older prototypes used in papers and for more advanced versions, please contact me.
This prototype is provided under GNU GPLv3, WITHOUT ANY WARRANTY.
A paper about the underlying algorithm: http://www.biomedcentral.com/1471-2105/14/S5/S8
Please cite as: Lederman, Roy. “A random-permutations-based approach to fast read alignment.” BMC Bioinformatics 14.Suppl 5 (2013): S8.