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Table 2 Workflow execution times estimated for three datasets

From: Automated identification of reference genes based on RNA-seq data

Species/tissue

No. raw reads

Mean length (nt)

No. transcripts

Pre-processing

Mapping

FindRGs

Total

Olive tree pistil

767,963

525

9157

24 min 45 s

26 s

5 s

25 min 16 s

8 nodes, 192 cpus

3 nodes, 72 cpus

1 node, 9 cpus

Arabidopsis

23,821,198 (x2)

100 (x2)

35,386

43 s

19 s

0.2 s

1 min 2 s

8 nodes, 192 cpus

2 nodes, 48 cpus

1 node, 9 cpus

Human prostate

969,884,666 (x2)

90 (x2)

176,241

28 s

2 min 37 s

0.03 s

3 min 5 s

96 nodes, 2304 cpus

24 nodes, 576 cpus

1 node, 9 cpus

  1. All time values are referred to 100,000 reads when executed on SUSE® Linux Enterprise Server v12 using Opteron processors with 4 GB/core of RAM