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Old 11-28-2011, 11:42 AM   #1
Location: St. Louis, MO

Join Date: Aug 2011
Posts: 53
Default pair_num_contigs in SOAPdenovo assembly

I'm running SOAPdenovo 1.05 and it seems to be ignoring when i set the pair_num_contigs parameter in the cfg file. I try setting this to 1 for my library and it shows up as 1 in .peGrads (0 for the others). However, during the scaffolding step, the log reports that it is running with the parameter set to 5 (the default for LIMP).

Has anyone gotten this parameter to work? Others have tried lowering and raising this parameter with little success:
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pair_num_contigs, scaffolding, soapdenovo

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