Research Article
CallSim: Evaluation of Base Calls Using Sequencing Simulation
Algorithm 1
The pseudocode for a single flow in the simulation process. The process is repeated for each flow that was produced during the sequencing process.
| signal:=
0
; # initialize the signal value | | for (all polymerase/molecules that are not stalled) | | { | | if (base == ‘N’) { skip over this base } | | else if (Rand < ) { polymerase status:= stalled } | | else while((base==flow base) & (!stalled) & (no failure to add base)) | | { | | if ( Rand > ) # add base | | { | | position++; # polymerase moves to next base | | signal++; # signal produced | | if (position == last base) { polymerase status:= stalled } | | } | | } | | } next polymerase/molecule |
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