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Old 03-13-2013, 09:16 AM   #3
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Location: NL, Leiden

Join Date: Feb 2010
Posts: 245

Check out CLC's white paper where their algorithm for assembly and scaffolding is explained;

For quality checking, one way is to map your paired-reads back to your assembly (there is an option for this in CLC Workbench). The higher number of paired-reads that could be mapped back to your contigs/scaffolds, the better the assembly. In addition, the N50 and number of contigs is also a way to check the quality. Although this does not tell you if there is any misassembly.

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