Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.

ABSTRACT:

Motivation

Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is the recently proposed GenASM algorithm. We identify and address three inefficiencies in the GenASM algorithm: it has a high amount of data movement, a large memory footprint, and does some unnecessary work.

Results

We propose Scrooge, a fast and memory-frugal genomic sequence aligner. Scrooge includes three novel algorithmic improvements which reduce the data movement, memory footprint, and the number of operations in the GenASM algorithm. We provide efficient open-source implementations of the Scrooge algorithm for CPUs and GPU

SUBMITTER: Lindegger J 

PROVIDER: S-EPMC10191611 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature