Pblat: a multithread blat algorithm speeding up aligning sequences to genomes.

ABSTRACT:

Background

The blat is a widely used sequence alignment tool. It is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. However, the blat tool is single threaded and when used to map whole genome or whole transcriptome sequences to reference genomes this program can take days to finish, making it unsuitable for large scale sequencing projects and iterative analysis. Here, we present pblat (parallel blat), a parallelized blat algorithm with multithread and cluster computing support, which functions to rapidly fine map large scale DNA/RNA sequences against genomes.

Results

The pblat algorithm takes advantage of modern multicore processors and significantly reduces the run

SUBMITTER: Wang M 

PROVIDER: S-EPMC6334396 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature