Skip to main content

Table 2 Comparison of PathoScope 2.0 against other methods with ELISA positive fecal samples

From: PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples

 

STEC Genome/Plasmid Rank (Plasmid Rank)

Computation time (h:min)

Sample ID

PathoScope 2.0

PathoScope 1.0

ReadScan

RINS

PathoScope 2.0

PathoScope 1.0

ReadScan

RINS

Rank

Proportion

Rank

Proportion

Rank (Plasmid)

Rank

2535.1a

1

39.4%

1

40.3%

9 (1)

8

8:29

7:21

16:46

1:27

2535.2

1

91.4%

1

87.8%

8 (1)

13

0:19

0:14

0:27

22:43

2535ba

1

36.9%

1

37.6%

13 (1)

36

2:47

2:25

7:26

1:26

2638

1

99.8%

1

95.7%

5 (1)

38

1:17

1:06

1:11

19:25

2661

1

95.7%

1

91.4%

8 (1)

7

0:36

0:32

1:58

8:57

2668

1

73.5%

1

85.3%

10 (1)

DNF

0:01

0:01

0:29:15

>24:00

2723b

1

99.8%

1

94.1%

5.5 (1)

37

0:14

0:12

0:43

15:28

2741

4

2.9%

28

0.0%

26 (1)

DNF

0:48

0:38

1:21:08

>24:00

2752

1

65.5%

2

10.1%

13 (1)

20

0:09

0:08

0:49

18:20

2758

1

99.7%

1

93.8%

8 (1)

38

0:16

0:15

0:52

10:13

2764

1

99.4%

1

96.6%

7 (1)

6

0:15

0:14

1:06

5:47

2772

1

99.6%

1

94.0%

4 (1)

8

0:00

0:00

0:16

12:22

2828

2

26.5%

2

5.3%

16 (1)

36

0:18

0:15

0:52

4:18

2840

1

99.5%

1

94.2%

8 (1)

14

1:52

1:40

1:58

19:08

2848

3

2.1%

6

0.7%

35 (3)

DNF

0:14

0:11

0:48

>24:00

2849

1

99.7%

1

95.2%

8 (1)

27

0:28

0:24

1:12:40

2:16:27

2878

1

99.4%

1

93.6%

8 (1)

DNF

0:07

0:06

1:04

>24:00

2880

1

87.9%

1

90.5%

11 (1)

37

0:04

0:04

0:26:33

2:35:38

2896

1

99.9%

1

95.2%

3 (1)

14

0:43

0:34

1:36:33

10:51:35

2971

1

99.9%

1

93.3%

8 (1)

38

0:23

0:19

0:56:59

5:05:27

3014

1

99.7%

1

92.3%

7 (1)

DNF

0:34

0:31

1:07:34

>24:00

3093

1

100.0%

1

88.7%

7 (1)

20

0:00

0:00

0:21:46

0:25:38

3132

1

96.5%

1

89.8%

15 (1)

11

0:07

0:06

1:36:49

8:56:37

3134

2

28.0%

2

5.8%

26 (1)

38

0:19

0:16

0:48:50

2:00:25

3135

1

99.7%

1

93.2%

8 (1)

DNF

0:12

0:10

0:58:49

>24:00

3185

1

91.4%

1

89.4%

9 (2)

6

0:22

0:19

0:51:03

17:34:13

3303

1

99.4%

1

94.2%

8 (1)

37

0:13

0:10

0:42:17

0:27:51

3549

8

0.7%

12

0.4%

65 (8)

9

0:11

0:09

0:41:51

20:41:23

3587

2

5.8%

3

2.5%

20 (7)

DNF

0:10

0:09

1:04:31

>24:00

3646

17

0.0%

5

1.2%

57 (19)

20

0:07

0:05

1:11:30

0:43:05

3751

2

5.8%

2

2.9%

19 (3)

DNF

0:22

0:19

1:11:05

>24:00

3852

1

100.0%

1

92.4%

5 (1)

13

0:00

0:00

0:18:15

1:08:41

3958

3

2.9%

5

1.1%

64 (7)

9

0:05

0:05

0:41:53

10:33:13

4112

7

0.7%

3

2.8%

50 (6)

38

0:08

0:08

0:41:39

13:05:36

4141

1

74.7%

1

83.5%

28 (2)

NI

0:03

0:03

1:01:14

10:57:57

4168

1

100.0%

1

95.2%

2 (1)

13

0:00

0:00

0:08:43

6:29:11

4198

2

1.4%

3

0.8%

36 (11)

37

0:43

0:33

1:20:30

12:17:53

4328b

1.5

21.7%

1

87.0%

7.5 (2)

DNF

0:05

0:05

0:56

>24:00

4508

3

6.5%

3

2.2%

37 (8)

38

0:05

0:04

0:44:12

14:44:41

5066

17

0.1%

13

0.2%

14 (1)

DNF

0:06

0:05

0:26:53

>24:00

  1. aUsed different parameters for bowtie2 alignment: ‘--very-sensitive-local --score-min L,280,0.0 -k 10’.
  2. bThere are multiple sequencing runs for this sample, so the results were averaged across replicates.
  3. DNF: the algorithm did not finish in less than 24 h on a 16 cpu compute node; NI: the STEC O104:H4 genome was not identified by the method.
  4. These are the results from the O104:H4 study - Positive Samples. See the section titled ‘Evaluation and comparison on clinical sequencing samples’ for details.
Back to article page

Microbiome

ISSN: 2049-2618

Contact us