MP-LAMP: Parallel Detection of Statistically Significant Multi-Loci Markers on Cloud Platforms.

ABSTRACT: Exhaustive detection of multi-loci markers from genome-wide association study datasets is a computationally challenging problem. This paper presents a massively parallel algorithm for finding all significant combinations of alleles and introduces a software tool termed MP-LAMP that can be easily deployed in a cloud platform, such as Amazon Web Service, as well as in an in-house computer cluster. Multi-loci marker detection is an unbalanced tree search problem that cannot be parallelized by simple tree-splitting using generic parallel programming frameworks, such as Map-Reduce. We employ work stealing and periodic reduce-broadcast to decrease the running time almost linearly to the number of cores.MP-LAMP is available at https://github.com/tsudalab/[e-mail] data are available at Bioinformatics online.

SUBMITTER: Yoshizoe K 

PROVIDER: S-EPMC6129301 | biostudies-other | 2018 Apr

REPOSITORIES: biostudies-other