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Old 04-17-2017, 08:29 AM   #1
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Location: Czech republic

Join Date: Mar 2017
Posts: 1
Default multiple occuring element cause problem with scaffolding


I have problem with scaffolding. I tried to combine Spades and SSpace but after several failures a gave it up. I realized that the problem may be in the IS element which occurs several times in genome of sequenced bacteria. I try blast this IS element in Spades output graph I found this branching. Any idea what to do?
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illumina miseq, ngs, repetitive elements, scaffolding

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