Default sequencing keys and flow order

Question

[alok.helix]

Please explain to me the algorithm, the concept of "keys" and flow order use in Ion torrent PGM machine during Analysis pipeline module of PGM

The following table shows the default library and TF sequencing keys in both base-space and flow-space for the default,TACG,flow order:

                                     Flow Order TACG Vector
Library Key:TCAG          1010010X (Does 1 indicate incorporation of base T?)
TF Key:      ATCG          0100101X

The "X" in the vector column indicates that the value is at least a one, but could in fact be higher because the next base after the key could also match, thus creating a longer homopolymer.

[Zaag]

A key is a 4 base sequence with all 4 different bases that the machine uses to normalize the signal for each base. After the key it knows the signal for 1 incorporated base of each kind.

Can't help you with the rest.