Base caller algorithms
Two algorithms are currently available for the base caller: the Average method and the Max value method. They are defined in the Options dialog.
In both methods, a threshold level is computed.
Average
The average level of each nucleotide wave is computed. The greatest average multiplied by the base-caller % of higher peak given in the option dialog will give a threshold level.
Each nucleotide having a trace wave average value greater than or equal to the threshold is considered as valid.
Max value
The highest point in each nucleotide wave is searched. The greatest value multiplied by the base-caller % of higher peak given in the option dialog will give a threshold level.
Each nucleotide having a trace wave average value greater than or equal to the threshold is considered as valid.
In both algorithms, the nucleotide letters are merged respecting the following table:
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G
|
Guanosine
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A
|
Adenosine
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T
|
Thymidine
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C
|
Cytidine
|
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R
|
G or A, puRine
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Y
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C or T, pYrimidine
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K
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G or T, Keto
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W
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A or T, Weak (2 H-bonds)
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S
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C or G, Strong (3 H-bonds)
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M
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A or C, aMino
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B
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C, G or T (i.e., not A)
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D
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A, G or T (i.e., not C)
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H
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A, C or T (i.e., not G)
|
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V
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A, C or G (i.e., not T)
|
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N
|
A, C, G or T, aNy
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X
|
A, C, G or T
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