Summary

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.

Availability and implementation

MP-LAMP is available at https://github.com/tsudalab/mp-lamp.

Supplementary information

Supplementary data are available at Bioinformatics online.

© The Author(s) 2018. Published by Oxford University Press.
2018
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