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An integrated approach to comparative assembly
(2014)
We describe a novel approach to comparative assembly that directly integrates anchoring alignments into the contig assembly process, enabling the extension of contig construction through the boundaries of repeat nodes in ...
Fast and accurate genome anchoring using fuzzy hash maps
(2011)
Although hash-based approaches to sequence alignment and genome assembly are long established, their utility is predicated on the rapid identification of exact k-mers from a hash-map or similar data structure. We describe ...
Approximate k-mer matching using fuzzy hash maps
(IEEE Computer Society, 2014)
We present a fuzzy technique for approximate k-mer matching that combines the speed of hashing with the
sensitivity of dynamic programming. Our approach exploits the collision detection mechanism used by hash maps, unifying ...
A java library for fuzzy string matching
(2012)
We describe the design and structure of a Java library for approximate string matching. The API provides a rich variety of flexible and extensible fuzzy data structures, including lists, tries and maps that support approximate ...