mrsFAST: a cache-oblivious algorithm for short-read mapping

In addition to single-nucleotide variations and small insertions-deletions (indels), largersized structural variations (for example, insertions, deletions, inversions, segmental duplications and copy-number polymorphisms) contribute to human genetic diversity. In almost all recent structural variation discovery (SVD) studies, short reads from a donor genome have been mapped to a reference genome as a first step. The accuracy of such an SVD study is directly correlated to the accuracy of this mapping step, which also provides the main computational bottleneck of the SVD study.