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

ABSTRACT:

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 3.5 and 5.3 GB for a human reference genome for typical parameter settings. The succinct hash index features two novel seed selection algorithms (group seeding and variable-length seeding) and an efficient parallel construction algorithm, which we have implemented to design the FEM (Fast(F) and Efficient(E) read Mapper(M)) mapper. FEM can return all rea

SUBMITTER: Zhang H 

PROVIDER: S-EPMC5845352 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature