Can the Geneious assembler do scaffolding?

From R8 onwards, the Geneious de novo assembler can be configured to produce scaffolds where contigs are linked by paired read information.  The missing region between contigs is filled by Ns.  To enable this option, you must first pair your reads by running “Set paired reads” under the “Sequence” menu.  Then go to De novo assemble, click More Options and check “Produce Scaffolds”.

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