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Table 2 Scores of algorithms when aligning short reads to REF-2

From: Mora: abundance aware metagenomic read re-assignment for disentangling similar strains

Algorithm

Species

Genus

F1

Sensitivity

Precision

F1

Sensitivity

Precision

Pufferfish

46.23

32.61

79.38

55.54

39.18

95.36

Mora + Pufferfish

47.79

33.72

82.06

56.00

39.50

96.15

AugPatho2 + Pufferfish

48.40

34.14

83.11

56.11

39.58

96.34

Bowtie2

64.08

52.36

82.58

74.96

61.24

96.59

Mora + Bowtie2

65.23

53.29

84.06

75.17

61.41

96.87

AugPatho2 + Bowtie2

66.10

54.01

85.18

75.27

61.24

96.99

Kraken2

70.28

66.32

74.73

88.54

83.55

94.15

Clark*

13.78

7.80

59.11

20.13

11.39

86.37

  1. On both aligners, Mora performed just a bit worse than AugPatho2, with scores having a difference of at most 1 when using Bowtie2. Mora’s scores are consistently better than the aligners, showing that the re-assignment step is beneficial. Kraken2 was able to map more reads compared to Mora and AugPatho2 due to mapping more reads than Pufferfish and Bowtie2. Clark has an asterisk to signify that its low scores are due to an issue with building the bacteria database
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BMC Bioinformatics

ISSN: 1471-2105

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