Gene

String (physics)

Algorithm

Mathematical physics

Biology

Reference genome

Operating system

Computation

Set (abstract data type)

Data mining

Computer science

Computational genomics

Computational biology

Genetics

Genome

Mathematics

Genomics

Artificial intelligence

Programming language

Pattern matching

String searching algorithm

Heuristics

Read mapping is a fundamental step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome (called a reference genome). Read mapping is costly because it needs to perform approximate string matching (ASM) on large amounts of data. To address the computational challenges in genome analysis, many prior works propose various approaches such as accurate filters that select the reads within a dataset of genomic reads (called a read set) that must undergo expensive computation, efficient heuristics, and hardware acceleration. While effective at reducing the amount of expensive computation, all such approaches still require the costly movement of a large amount of data from storage to the rest of the system, which can significantly lower the end-to-end performance of read mapping in conventional and emerging genomics systems.

GenStore: a high-performance in-storage processing system for genome sequence analysis