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Table 4 Summary of the computing resources required by each method.

From: Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Software

Time taken (mins)

Peak memory usage (GB)

GenomeStudio (v 1.1.0)*

230

0.75

GenoSNP†

370â‹„

0.09

Illuminus†

38â‹„

12.2

CRLMM (v 1.2.4)†

28

38.2

  1. These figures are based on the analysis of a set of 346 samples (batch 2) from the MS-GWAS.
  2. * run on a PC (Pentium quad core, 3 Ghz computer with 2 GB RAM) with file-based storage enabled
  3. † run on a quad-core AMD Opteron 2.7 Ghz CPU linux machine with 64 GB RAM
  4. â‹„ timing does not include time taken by GenomeStudio to output X and Y data used as input for these methods (30 mins and 0.65 GB RAM on the PC we used)
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BMC Bioinformatics

ISSN: 1471-2105

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