MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms.
basic_science · Level V
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- Record sourced from PubMed, PMID 29659720.
- Also identified by DOI 10.1093/bioinformatics/bty219 and PMC identifier 6129301.
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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/mp-lamp. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Cloud Computing