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Table 4 k -mers counting results for Caenorhabditis elegans (16.4 GB FASTQ file or 2 gzipped FASTQ files of total size 4.6 GB)

From: Disk-based k-mer counting on a PC

 

k=22

k=28

k=40

k=55

Algorithm

Space

Time

Space

Time

Space

Time

Space

Time

 

Classic counters

 

32-core server

BFCounter

4/ 0

10,407

Failed

Failed

Failed

Jellyfish

21/ 0

88

22/ 0

89

DSK

5/13

493

5/13

458

5/16

647

5/16

481

DSK gz

5/13

587

5/13

564

5/16

761

5/16

592

KMC

32/10

105

32/18

115

32/27

185

32/31

191

KMC

16/11

93

16/18

93

16/27

163

16/32

160

KMC gz

32/10

134

32/18

138

32/27

199

32/31

203

KMC gz

16/11

119

16/18

121

16/27

195

16/32

182

 

6-core PC

DSK

5/13

1,307

5/13

1,215

5/16

2,073

5/16

1,597

DSK gz

5/13

1,268

5/13

1,151

5/16

2,017

5/16

1,518

KMC

11/11

274

11/18

343

11/27

507

11/32

553

KMC gz

11/11

233

11/18

333

11/27

514

11/32

542

 

Quake-compatible counters

 

32-core server

BFCounter

4/ 0

10,349

4/ 0

9,527

4/ 0

8,213

4/ 0

6,689

Jellyfish

24/ 0

143

25/ 0

132

KMC

32/31

173

32/37

179

32/42

245

32/43

243

KMC

16/32

166

16/37

154

16/43

212

16/44

214

KMC gz

32/31

184

32/37

188

32/43

247

32/43

249

KMC gz

16/32

168

16/37

165

16/43

218

16/44

230

 

6-core PC

KMC

11/32

562

11/37

635

11/43

750

11/44

784

KMC gz

11/32

555

11/37

627

11/43

749

11/44

772