Table 1

Myrna runtime, cost for 1.1 billion reads from the Pickrell et al. study [32]

EC2 nodes

1 master, 10 workers

1 master, 20 workers

1 master, 40 workers


Worker processor cores

80

160

320

Wall clock time

4h:20m

2h:32m

1h:38m

Cluster setup

4m

4m

3m

Align

2h:56m

1h:31m

54m

Overlap

52m

31m

16m

Normalize

6m

7m

6m

Statistics

9m

6m

6m

Summarize and Postprocess

13m

14m

13m

Approximate cost (location dependant)

$44.00/$49.50

$50.40/$56.70

$65.60/$73.80


Timing and cost for a Myrna experiment with 1.1 billion 35-bp unpaired reads from the Pickrell et al. study [32] as input. Costs are approximate and based on the pricing as of this writing, that is, $0.68 per High-CPU Extra Large instance per hour in the Northern Virginia zone and $0.78 elsewhere, plus a $0.12 per-node-per-hour surcharge for Elastic MapReduce. The table does not include the transfer of the read data from University of Chicago servers to S3, which takes a wall clock time of 1h:15 m and costs about $12. Other charges may apply and times may vary subject to, for example, congestion and Internet traffic conditions.

Langmead et al. Genome Biology 2010 11:R83   doi:10.1186/gb-2010-11-8-r83

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