Abstract: Disclosed methods pertain to nucleic acid shuffling techniques that employ repeated short extension cycles. In each such cycle, strand extension along a template fragment is limited such that the strand extends only for a relatively short length (e.g., a few base pairs). Repeated short extension cycles cause many template switches during shuffling and thereby produce chimeric products with many crossovers. The methods may employ a pre-shuffling truncation or excision operation in which one or more parent nucleic acids has a portion of its full-length sequence truncated or excised. Shuffling with truncated parent nucleic acids introduces crossovers at the location of the truncation. Apparatus for implementing the disclosed methods may include appropriately configured thermocycling tools.