Fast and efficient short read mapping based on a succinct hash index.

Background: Various indexing techniques have been applied by next generation sequencing read mapping tools. The choice of a particular data structure is a trade-off between memory consumption, mapping throughput, and construction time.

Results: We present the succinct hash index - a novel data structure for read mapping which is a variant of the classical q-gram index with a particularly small memory footprint occupying between 3.