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Table 3 k -mers counting results for Homo sapiens HG02057 individual (208 GB FASTQ file or 6 gzipped FASTQ files of total size 65.9 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

Jellyfish

27/ 0

1,375

75/ 0

1,433

—

—

Jellyfish1

27/ 0

1,375

21/ 53

2,404

—

—

DSK

6/168

8,683

6/156

9,073

6/195

13,172

6/197

9,409

DSK gz

6/168

10,125

6/156

10,579

6/195

14,569

6/197

10,987

KMC

32/130

1,221

32/220

1,706

32/341

2,486

32/391

2,722

KMC

16/134

1,376

16/234

1,872

16/343

2,664

16/405

2,967

KMC gz

32/130

1,249

32/219

1,505

32/342

2,304

32/391

2,597

KMC gz

16/134

1,195

16/234

1,732

16/343

2,479

16/403

2,909

 

6-core PC

DSK

6/168

22,963

6/156

23,512

6/195

37,958

6/197

28,681

DSK gz

6/168

21,688

6/156

22,061

6/195

36,328

6/197

26,584

KMC

11/137

2,939

11/234

3,782

11/343

6,133

11/405

7,770

KMC gz

11/136

2,623

11/235

4,041

11/343

6,306

11/405

7,020

 

Quake-compatible counters

 

32-core server

Jellyfish

51/ 0

2,426

59/126

2,503 ∗

—

—

KMC

32/388

2,612

32/468

3,011

32/537

3,541

32/542

3,546

KMC

16/402

2,990

16/468

3,405

16/539

4,300

16/552

4,175

KMC gz

32/387

2,409

32/468

2,860

32/537

3,370

32/536

3,357

KMC gz

16/400

2,760

16/468

3,285

16/498

4,083

16/552

4,038

 

6-core PC

KMC

11/404

6,625

11/469

7,741

11/539

9,673

11/552

11,135

KMC gz

11/403

6,783

11/468

8,034

11/539

9,764

11/553

9,775

  1. Test methodology and column description are just as for Table 2. The asterisk sign (for Jellyfish) denotes that two separate databases were constructed by Jellyfish due to the memory limit of the machine (128GB RAM) and Jellyfish reported that to merge these databases it needs more RAM, so these times are underestimated.
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BMC Bioinformatics

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