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Table 2 Run-time efficiency of tools for processing next-generation sequencing data

From: FastProNGS: fast preprocessing of next-generation sequencing reads

Tools

run-timec

rss (MB)d

vmem (MB)e

Average CPU utilization f

rchar(GB)g

wchar(GB)h

run-time/CPUi

Process .gzj

NGS QC Toolkit

344

3062

3400

3.312

88

54

1139

R + W

FASTX-Toolkit

308

10

29

1.556

60

46

479

W

PRINSEQ

252

20

115

1.173

177

99

296

–

Fastqc

7

395

2150

2.403

6

0

17

R

Cutadapta

4

670

1645

6.548

56

75

26

R

Cutadaptb

58

675

1659

1.605

84

84

93

R + W

FastProNGSb

3

7168

7291

6.396

6

22

19

R + W

FastProNGSa

13

7066

7270

6.008

6

4

78

R

FaQC

27

121

644

3.876

7

27

105

R

fastpa

8

723

1167

4.614

7

5

36

R + W

fastpb

7

720

1110

5.421

7

21

40

R

  1. All tools were installed locally and run against the test data set
  2. aOutput files are gzip-compressed
  3. bOutput files are not compressed
  4. cMinimum task execution time (minutes)
  5. dMean real memory (resident set) size of the process (MB)
  6. eMean virtual memory size of the process (MB)
  7. fAverage number of CPUs utilized by the process
  8. gNumber of bytes the process read (GB)
  9. hNumber of bytes the process wrote (GB)
  10. iMinimum task execution time using one CPU (minutes)
  11. jProcess .gz indicates if the test was natively read (R) or write (W) compressed files. ‘--’ indicates neither read or write compressed files