Table 3

Running time and memory usage of quantification methods on SE and PE data

SE

PE

Method

Alignment time

Quant. time

Total time

Peak Memory

Alignment time

Quant. time

Total time

Peak Memory


RSEM

24

50

74

1.1

15

50

66

1.1

IsoEM

5

6

12

12

14

10

24

14

Cufflinks

33

3

36

2.0

60

6

66

2.0

rQuant

33

183

216

2.0

RSEM v0.6

9

22

31

1.1


The alignment time, quantification time, total time, and peak memory usage of the tested quantification methods on SE and PE simulated data sets with 20 million fragments. Times are in minutes and memory is specified in GB.

Li and Dewey BMC Bioinformatics 2011 12:323   doi:10.1186/1471-2105-12-323

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