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Table 3 Compute resources required for de novo assembly

From: OMWare: a tool for efficient assembly of genome-wide physical maps

Assembly step

Sort

Split

Pairwise alignment

Assembly

Total

Applicable parameters

Minimum lengtha, minimum labelsa

Minimum lengtha, minimum labelsa

Minimum lengtha, minimum labelsa, significance thresholda, false positive, false negative

Minimum length, minimum sites, significance threshold, false positive, false negative

Minimum length, minimum sites, significance threshold, false positive, false negative

Steps run

1

1

9

405

-

Parallel jobs per step

1

3

1,250

1

-

Minutes elapsed

1

6

3,442,500

105,614

3,548,121

Predictedb minutes

405

2,733

154,912,500

105,614

155,021,252

Megabytes RAM used

1

5,667

176,321,250

1,130,838,484

1,307,165,402

Predictedb megabytes

405

2,295,135

7,934,456,000

1,130,838,484

9,067,590,024

Megabytes disk space used

580

580

4,640,000

51,874

4,693,034

Predictedb megabytes

2,900

2,900

208,800,000

51,874

209,089,674

  1. aInput parameter applies only as an output filter; it does not affect the algorithms internal workings. A step run with lenient parameters can serve as input for a more stringent downstream step, which will filter its input
  2. bEstimation of resources required if all 405 Sort, Split, and Pairwise alignment steps were run