GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

ABSTRACT:

Motivation

High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an ov

SUBMITTER: Alser M 

PROVIDER: S-EPMC5860160 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature