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Table 2 mmseq performance. Performance of the mmseqprogram on subsets of different sizes of the HapMap paired-end dataset.

From: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

Read pairs (millions)

Dimension of M

Runtime (seconds)

1

63,924 × 68,666

507

2

84,417 × 75,649

541

3

97,576 × 79,035

746

4

107,344 × 81,289

793

8

134,489 × 86,528

1,047

16

166,100 × 91,023

1,204

  1. Where necessary in order to obtain a large enough dataset, reads from multiple lanes of the same individual were pooled. The program exhibits economies of scale because the dimension of M increases more slowly than the number of reads.
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Genome Biology

ISSN: 1474-760X

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