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E-MEM / Efficient computation of Maximal Exact Matches
Provides a practical solution for finding MEMs between arbitrarily large genomes. E-MEM uses much less memory than the currently available programs. This algorithm uses much less space and is highly amenable to parallelization. It can compute all MEMs of minimum length 100 between the whole human and mouse genomes on a 12 core machine in 10 min and 2 GB of memory; the required memory can be as low as 600 MB. It can run efficiently genomes of any size.
Provides a software tool for constructing enhanced suffix arrays (ESAs) from biological sequence data. mkESA is a portable, lightweight and multithreaded program for constructing enhanced suffix arrays. It is also able to generate output compatible with mkvtree. It employs the ‘Deep-Shallow’ algorithm for suffix array construction. This algorithm belongs to the family of ‘lightweight’ suffix sorting algorithms, covering algorithms that use only very small additional space besides the suffix array and the input text.
BPR / Bucket-Pointer Refinement
Provides a suffix array construction algorithm. BPR is a simple structured method, easily implemented, that combines the approaches of refining groups with equal prefixes by recursively performing radix steps and the pull technique. It consists of two phases: (i) given a parameter, the suffixes are lexicographically sorted and (ii) the buckets containing suffixes with equal prefixes are recursively refined. It can be widely used in all kinds of suffix array applications.
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