Random-Permutations-Based Aligner (Prototype)
This is a basic example implementation of a Random-Permutations-Based Aligner/Mapper (RPA P3 / RPM P3).
Download: rpa_p3 (for the up to date version, please link to this page, and not directly to the file).
Please read the readme.txt file and try to run the examples.
Note: mapping to a full unmasked human reference genome may require slightly more than 16GB of RAM. Smaller references require less RAM. Spare RAM can be used for faster processing. For information about more efficient versions, please contact me.
This is a SIMPLIFIED PROTOTYPE. It is provided under GNU GPLv3, WITHOUT ANY WARRANTY.
For the older prototypes used in papers and for more advanced versions, please contact me.
Please contact me with any questions or problems with the prototype.
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.