▁It ▁is ▁suggested ▁to ▁run ▁Pic ard ▁Mark D up licates ▁as ▁follows : ▁ ▁java ▁- jar ▁pic ard . jar ▁Mark D up licates ▁I = input . b am ▁O = mark ed _ dup licates . b am ▁M = mark ed _ dup _ met rics . txt ▁RE AD _ NAME _ RE GE X = null ▁ ▁A ▁test ▁with ▁Pic ard - friend ly , ▁reform atted ▁read ▁names ▁demonstr ates ▁the ▁absence ▁of ▁this ▁class ▁of ▁duplicate ▁read : ▁ ▁The ▁single ▁read ▁marked ▁as ▁an ▁optical ▁duplicate ▁is ▁most ▁assured ly ▁arte fact ual . ▁In ▁any ▁case , ▁the ▁effect ▁on ▁the ▁estimated ▁library ▁size ▁is ▁neg lig ible . ▁ ▁Adv antages ▁ ▁DNA ▁nan ob all ▁sequ encing ▁technology ▁offers ▁some ▁advantages ▁over ▁other ▁sequ encing ▁platforms . ▁One ▁ ▁advantage ▁is ▁the ▁er adic ation ▁of ▁optical ▁duplicates . ▁DNA ▁nan ob alls ▁remain ▁in ▁place ▁on ▁the ▁pattern ed ▁array ▁and ▁do ▁not ▁inter f ere ▁with ▁neighbor ing ▁nan ob alls . ▁ ▁Another ▁advantage ▁of ▁DNA ▁nan ob all ▁sequ encing ▁include ▁the ▁use ▁of ▁high - f idel ity ▁Ph i ▁ 2 9 ▁DNA ▁polym er ase ▁to ▁ensure ▁accurate ▁ampl ification ▁of ▁the ▁circular ▁template , ▁several ▁hundred ▁copies ▁of ▁the ▁circular ▁template ▁compact ed ▁into ▁a ▁small ▁area ▁resulting ▁in ▁an ▁inten se ▁signal , ▁and ▁attachment ▁of ▁the ▁flu or oph ore ▁to ▁the ▁pro be ▁at ▁a ▁long ▁distance ▁from