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Table 3 Comparison on 13 sets of programs and parameters using 100 bp paired-end simulated reads.

From: MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

6M 100 bp Paired-end reads, 1.2 Gbp bases. 500 bp insert size, 25 bp standard deviation.

MIC

GPU

CPU

   

MICA(1 MIC Card, 240 threads)

SOAP3-dp

SOAP3

Bowtie2

(Sensititve)

Bowtie2

(Very-Sensititve)

Bowtie2

(Very-fast)

BWA1

SeqAlto

SeqAlto

(Fast alignement)

CUSHAW2

GEM2

GEM2

(Fast Mapping: adaptive)

GEM2

(Fast Mapping: 0)

Configuration

CPU (thread: core i7-3930k)

1

4

4

4

4

4

4

4

4

4

4

4

4

 

GPU (device: GTX680)

0

1

1

0

0

0

0

0

0

0

0

0

0

Computational Resources

Total Elapsed

sec.

178

162

132

966

1974

672

1154

495

379

1303

416

446

298

  

Fold

0.76

1.23

1.00

7.32

14.95

5.09

8.74

3.75

2.87

9.87

3.15

3.38

2.26

 

Loading Index3

sec.

83

74

74

38

38

38

53+1+1

96

96

40

40+1

40+1

40+1

 

Alignment4

sec.

95

88

58

928

1936

634

370+369+360

399

283

1263

199+176

238+167

90+167

  

Fold

0.95

0.88

0.58

9.28

19.36

6.34

10.99

3.99

2.83

12.63

3.75

4.05

2.57

 

Avg. Memory

GB

25.2

17.2

17.3

3.3

3.3

3.3

3.5

7

6.9

3.6

4.3

4.3

4.3

 

Peak Memory

GB

29.9

18.1

19.2

3.5

3.5

3.5

4.8

7.2

7.2

3.6

4.3

4.3

4.3

Alignment Metrics

Aligned

#

11,999,810

11,999,827

11,870,740

11,999,763

11,999,936

11,998,226

11,998,804

12,000,000

11,995,872

11,999,975

11,999,763

11,999,484

11,995,422

  

Diff.

-

17

-129,070

-47

126

-1,584

-1,006

190

-3,938

165

-47

-326

-4,388

 

Properly Paired

#

11999668

11,999,460

11,742,902

11,998,912

11,999,344

11,996,528

11,997,254

11,999,976

11,995,410

11,977,218

11,998,994

11,997,702

11,991,992

  

Diff.

-

-208

-256766

-756

-324

-3140

-2414

308

-4258

-22450

-674

-1966

-7676

 

Incorrectly Aligned

#

48,184

40,561

138,655

143,012

141,373

147,764

85,297

95,672

99,243

99,243

56,514

61,642

61,887

  

Diff.

-

-7,623

90,471

94,828

93,189

99,580

37,113

47,488

51,059

51,059

8,330

13,458

13,703

 

Sensitivity5

%

99.60%

99.66%

97.77%

98.81%

98.82%

98.75%

99.28%

99.20%

99.14%

99.17%

99.53%

99.48%

99.45%

  

Diff.

-

0.06%

-1.83%

-0.79%

-0.78%

-0.85%

-0.32%

-0.40%

-0.46%

-0.43%

-0.07%

-0.12%

-0.15%

 

FDR6

%

0.40%

0.34%

1.17%

1.19%

1.18%

1.23%

0.71%

0.80%

0.83%

0.83%

0.47%

0.51%

0.52%

  

Diff.

-

-0.06%

0.77%

0.79%

0.78%

0.83%

0.31%

0.40%

0.43%

0.43%

0.07%

0.11%

0.12%

  1. 1 The time consumption of BWA is calculated as "align left reads"+"align right reads"+"sampe". The index loading times of "align right reads" and "sampe" modules are 1 second due to the reason that, index files were cached during "align left reads". However, datasets larger than the host memory will flush the cache during alignment.
  2. 2 The alignment time consumption of GEM is calculated as "alignment"+"convert to SAM format". The conversion module was run with 4 threads in consistent with the alignment module.
  3. 3 SOAP3-dp, SOAP3, SeqAlto and GEM aligners explicitly provide index loading time consumption. The index loading time for Bowtie2, CUSHAW2 and BWA are calculated by the total size of index, divided by 100 MB/s, which is the average network file system speed of the testing environment. The index loading time maybe underestimated while the time processing the index was not calculated.
  4. 4 The alignment times were explicitly provided by the aligners (include results processing and input/output time) or calculated by total elapsed time minus estimated index loading time.
  5. 5 Sensitivity is calculated as "Correctly aligned reads"/"All simulated reads". The higher the better.
  6. 6 FDR is calculated as "Incorrectly aligned reads"/"All aligned reads". The lower the better
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BMC Bioinformatics

ISSN: 1471-2105

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