In this week’s Genome Biology, Niall Lennon and his Broad Institute colleagues present a scalable, fully automated process for the construction of sequence-ready barcoded libraries for use with 454 technology. Lennon and his colleagues devised a method that minimizes sample-handling errors and cross-contamination by using the end-to-end barcoding of plasticware and the molecular DNA barcoding of constructs. The team also describes their automation-friendly clean-up steps utilizing magnetic bead-based size selection, which further eliminate potential sources of error.