The realignContigs command causes SeqMan NGen to perform another pass through a reference-guided assembly once the initial assembly is complete, and realigns contigs as needed. (This step occurs automatically for de novo assemblies.) Using this command may improve the accuracy of the final assembly by correcting occasional misalignments that can occur in gapped regions, however note that this step may significantly increase the time to assemble. This command must appear in the script after the assemble command.
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