Table 1 Summary of varVAMP designs for tiled sequencing

From: varVAMP: degenerate primer design for tiled full genome sequencing and qPCR

Alignment statistics

varVAMP parameters

varVAMP output

Virus

Subtypes

n sequences

% mean sequence identity

Max ambig bases

Threshold

Optimal amplicon size

Maximum amplicon size

Expected recovery

n amplicons

varVAMP version

SARS-CoV-2

B.1 - XBB

865

99 ± 1

1

0.99875

700

800

99.72%

55

v.0.9.4

BoDV-1

all

55

89 ± 8

2

0.94

400

550

98.6%

27

v.0.6

HAV

all

309

81 ± 10

4

0.93

1000

1600

95.65%

7

v.0.8.3

HEV genotype 3

f, e

376

76 ± 6

4

0.91

1000

1500

99.02%

7

v.0.8.2

HEV genotype 3

c, h1, m, i, uc, l

201

75 ± 9

4

0.90

1000

1500

99.28%

6

v.0.8.2

PV

1-3

944

71 ± 13

4

0.91

1000

1400

99.63%

7

v.0.8

ratHEV

all

41

57 ± 10

5

0.82

1200

1700

97.41%

6

v.0.8.3

  1. The table lists important alignment statistics, varVAMP input parameters and output information including the varVAMP version. Pairwise sequence identity was calculated with Identity (https://github.com/BioinformaticsToolsmith/Identity). Max. ambig. bases (-a parameter): Maximum number of ambiguous characters that are allowed within a primer sequence. varVAMP outputThreshold (-t parameter): Identity frequency threshold for a consensus nucleotide. All primers and their respective varVAMP outputs are accessible at: https://github.com/jonas-fuchs/ViralPrimerSchemes.
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