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Table 3 Comparison of PathoScope 2.0 against alternatives with ELISA negative 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

1253

3

1.4%

8

0.3%

33 (2)

38

0:03

0:03

0:41

18:10

4961

7

0.3%

6

0.6%

40 (11)

38

1:16

0:59

1:09:37

23:58:39

1122

14

0.0%

2

7.3%

24 (1)

38

0:00

0:00

0:21:43

 

1196

NI

0.0%

2

3.0%

38 (1)

7

0:13

0:11

2:45:37

4:19:29

4096

25

0.0%

8

0.6%

70 (6)

14

0:07

0:06

0:29:09

0:06:00

1196b

4

0.8%

3

3.1%

31 (29)

9

0:04

0:04

1:27:27

7:03:26

4961b

8

0.2%

4

0.5%

35 (16)

39

0:15

0:12

0:30:49

21:30:20

1122b

15

0.0%

2

6.6%

26 (2)

38

0:03

0:02

0:17:41

5:32:59

4096b

22

0.0%

8

0.4%

76 (7)

36

0:01

0:01

0:14:37

0:18:45

  1. NI: the STEC O104:H4 genome was not identified by the method.
  2. These are the results from the O104:H4 study - Negative Samples. See the section titled ‘Evaluation and comparison on clinical sequencing samples’ for details.