ARC -- Assembly by Reduced Complexity ARC is a pipeline which facilitates iterative, reference-guided de novo assemblies with the intent of: - Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. - Reducing/removing reference bias as compared to mapping-based approaches. The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discrete 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.