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Parallel Mapping Approaches for GNUMAP.

ABSTRACT: Mapping short next-generation reads to reference genomes is an important element in SNP calling and expression studies. A major limitation to large-scale whole-genome mapping is the large memory requirements for the algorithm and the long run-time necessary for accurate studies. Several parallel implementations have been performed to distribute memory on different processors and to equally share the processing requirements. These approaches are compared with respect to their memory footprint, load balancing, and accuracy. When using MPI with multi-threading, linear speedup can be achieved for up to 256 processors.

SUBMITTER: Clement NL

PROVIDER: S-EPMC3565456 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Parallel Mapping Approaches for GNUMAP.

Clement Nathan L NL Clement Mark J MJ Snell Quinn Q Johnson W Evan WE

Proceedings. IPDPS (Conference) 20110101

Mapping short next-generation reads to reference genomes is an important element in SNP calling and expression studies. A major limitation to large-scale whole-genome mapping is the large memory requirements for the algorithm and the long run-time necessary for accurate studies. Several parallel implementations have been performed to distribute memory on different processors and to equally share the processing requirements. These approaches are compared with respect to their memory footprint, lo ...[more]

PMID: 23396612

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