Table 4

Memory requirements for real data

S. pneumoniae

E. coli

P. falciparum

index(Mb)

RAM(Mb)

index(Mb)

RAM(Mb)

index(Mb)

RAM(Mb)


BWA-SW

3

27

7

29

34

59

SSAHA2

517

788

521

773

552

717

Newbler

n/a

600

n/a

900

n/a

500

Segemehl

31

302

68

328

315

447

GASSST

n/a

2381

n/a

2479

n/a

2539

TAPyR 50

4

7

8

18

39

64


C. elegans

D. pseudoobscura

H. sapiens

index(Mb)

RAM(Mb)

index(Mb)

RAM(Mb)

index(Mb)

RAM(Mb)


BWA-SW

144

149

210

208

118

103

SSAHA2

679

1559

755

1209

648

680

Newbler

n/a

5100

n/a

2300

n/a

500

Segemehl

1388

2439

2025

2643

1134

1299

GASSST

n/a

5657

n/a

6967

n/a

4752

TAPyR 50

168

270

244

394

137

220


Memory requirements for the real biological data sets of Table 1. Shown are the index file size (when applicable) and peak main memory usage as measured by the tool tstime

http://bitbucket.org/gsauthof/tstime webcite, except for Newbler, whose overall memory demand was estimated through the Linux htop tool.

Fernandes et al. BMC Bioinformatics 2011 12:163   doi:10.1186/1471-2105-12-163

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