Parameter Name | Variable | Default Value | Parameter Range | Description |
---|---|---|---|---|

PCR_DISTRIBUTION | default | {default, none, file} | parameter specifies the name of a PCR distribution file, or 'default' to use a distribution with 15 rounds and 20 bins. A value of 'none' disables PCR amplification. | |

PCR_PROBABILITY | 0.7 | duplication probability in each step of the simulated PCR. The parameter value is only taken into account if GC_MEAN is 'NaN'. | ||

GC_MEAN | mean_{GC} | 0.5 | NaN, 0 < mean_{GC} < 1 | mean of duplication probability distribuiton with respect to GC content; the distribution is approximated by a normal distribution. A value of 'NaN' disables the GC-dependency of PCR and employs the (constant) probability PCR_PROBABILITY |

GC_SD | SD_{GC} | 0.1 | 0 < SD_{GC} < 1 | standard deviation of duplication probability distribuiton with respect to GC content |

The efficiency of the polymerase chain reaction (PCR) amplification is either specified by an universal success rate , or, by a normal distribution parameterized to capture GC preferential biases (default*mean*_{GC}=0.5 and *SD*_{GC}=0.1). Given *p*, the number of copies produced from a certain fragment is determined by random sampling under the cumulative binomial:

with *S* denoting the PCR cycle and *N* the number of molecules. As default, we assume 15 PCR cycles (*S*=15), and sample randomly the number of duplicates yielded by PCR amplification under the corresponding probability distribution P_{15}(*N*) for all possible values of *N*=[1;2^{15}]. The recursion terminates by

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