(a) Diagram illustrating design and usage of custom sequencing adapters that implement two types of molecular barcodes. Shown are the initial molecule to which adapters are ligated (left), the two molecules derived from one round of PCR applied to the original molecule (top right), and the sequencing reads derived from these two post-PCR molecules (bottom right). Index and insert barcode types are indicated by blue/red and purple/green blocks, respectively. The sample multiplexing barcode is indicated in orange. (b) Comparison of selector-wide error rates and base substitution distributions across 12 healthy control cfDNA samples (Supplementary Table 2) for the following methods: no barcoding or polishing, index barcode de-duplication, insert barcode de-duplication (with and without considering duplex-supported barcodes), insert barcode followed by index barcode de-duplication (insert–index; here, singleton variants were ignored for insert de-duplication and were only eliminated if not supported by an index barcode family with ≥2 members), and duplex-only de-duplication (i.e., only molecules with both strands of the original duplex). Error bars represent s.e.m. (c) CAPP-Seq libraries were made from 12 healthy control cfDNA samples (Supplementary Table 2), and the libraries were sequenced with and without the inclusion of 10% PhiX during sequencing. In addition, CAPP-Seq libraries were made from seven different healthy control cfDNA samples using staggered insert barcodes—four with short and three with long barcodes (Methods). The selector-wide error rates for each of these 31 samples are shown. Errors in b,c were determined as described in Calculation of selector-wide error profiles in Methods. Group comparisons were performed with a paired two-sided t test (**, P < 1.4×10−10; *, P < 0.03).