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Table 1 Memory and runtime for Illumina and Roche/454 simulations

From: GemSIM: general, error-model based simulator of next-generation sequencing data

Program, data

Memory (Gb)

Runtime (h:min)

Data processed (bases)

GemErr, Illumina v4

0.34

3:15

0.9 × 108

GemErr, Illumina v5

0.34

4:23

1.1 × 108

GemErr, Roche/454

0.39

0:20

1.3 × 107

GemReads, Illumina v4

0.44

3:08

5.0 × 108

GemReads, Illumina v5

0.46

3:10

5.0 × 108

GemReads, Roche/454

0.46

2:45

4.0 × 108

  1. Memory requirements and runtime are given separately for the two main programs within the GemSIM workflow, GemErr and GemReads. Both programs were run on a single Intel Xeon E5530 2.4 GHz CPU. To facilitate comparison, the number of bases processed to create the error models is given for GemErr, while the number of simulated bases is given for GemReads. For the simulations, all reads were generated from the same set of B. aphidicola haplotypes (created with GemHaps) using the appropriate error model.
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BMC Genomics

ISSN: 1471-2164

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