Home - readmapping/essaMEM GitHub Wiki

Welcome to the essaMEM wiki! essaMEM is an algorithm for calculating maximal exact matches using enhanced sparse suffix arrays.

Algorithms for calculating maximal exact matches, used in genome comparisons and read mapping, rely on memory-efficient index structures such as suffix arrays supplemented with auxiliary information. We further enhance an existing sparse suffix array with a sparse child array. Tests indicate that the enhanced algorithm for calculating maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.

Installation instructions and usage can be found in on the usage page.

The sequences used in testing essaMEM can be found either found here, or downloaded from the UCSD Genome Browser Download Page, or from the SRA archive.

In addition to the code, readme and Makefile, the essaMEM repository contains a tar bal with the latest stable build of essaMEM.

Copying information and license agreement can be found here. essaMEM enhances an implementation of sparse suffix arrays:sparseMEM and is thus also licensed under the license agreement of sparseMEM:

Don't hesitate to contact us at michael.vyverman[at]ugent.be if you have any further questions or suggestions.