End repair of contigs from Flye #4
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Added a shell script that performs a modified version of the circlator pipeline. Takes raw Nanopore reads as input and uses Flye to assemble the stitch region across circular contigs. The circlator merge module is used to integrate the stitch region and the assembly. This corrects the mid-scale indel errors (10's of bases) that are known to occur at the end of circular Flye contigs.