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Table 3 Performance statistics (A4, A5, S4, S5: simulated; C1, C2, PA: real)

From: CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing

Tool

dataset (# reads)

# merges

# correct merges

time (sec)

accuracy

F 1

dataset (# reads)

# merges

# correct merges

time (sec)

accuracy

F 1

CASPER

 

999,936

967,842

30

0.968

0.984

 

713,782

667,421

23

0.932

0.965

COPE

A4

262,661

241,630

183

0.242

0.389

C1

603,357

572,885

205

0.800

0.889

FLASH

(1,000,000)

989,960

732,040

20

0.732

0.845

(716,366)

688,730

601,561

22

0.840

0.913

PANDAseq

 

991,698

807,691

6

0.808

0.894

 

693,518

590,898

5

0.825

0.904

CASPER

 

999,973

997,201

30

0.997

0.999

 

1,345,759

1,233,831

40

0.914

0.955

COPE

A5

924,634

915,981

205

0.916

0.956

C2

1,105,743

1,046,420

319

0.775

0.873

FLASH

(1,000,000)

999,578

977,355

19

0.977

0.989

(1,350,602)

1,282,916

1,101,436

35

0.816

0.898

PANDAseq

 

999,101

978,527

6

0.979

0.989

 

1,298,903

1,080,593

9

0.800

0.889

CASPER

 

1,000,000

960,986

29

0.961

0.980

 

671,877

658,631

19

0.977

0.989

COPE

S4

262,107

230,595

181

0.231

0.375

PA

[COPE does not run on PA]

FLASH

(1,000,000)

999,964

697,867

18

0.698

0.822

(673,845)

660,984

634,261

16

0.941

0.970

PANDAseq

 

999,976

785,919

5

0.786

0.880

 

660,593

635,663

4

0.943

0.971

CASPER

 

1,000,000

997,303

28

0.997

0.999

      

COPE

S5

974,219

961,366

162

0.961

0.980

      

FLASH

(1,000,000)

999,921

977,431

19

0.977

0.989

      

PANDAseq

 

999,947

976,701

6

0.977

0.988

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