In addition to the updated protocol, we also include a comprehensive computational pipeline that we use to process and analyze our data (Fig. 2). The computational workflow for DS uses a number of standard software packages to process the sequencing data; these include the Burrows-Wheeler Aligner (BWA)37, SAMtools38, Picard and the Genome Analysis Toolkit (GATK)39,40, as well as several custom Python scripts. The computational workflow is broken down into three major steps: (i) Tag parsing and initial alignment; (ii) SSCS assembly; and (iii) DCS assembly. The latest version of the DS software package can be downloaded from https://github.com/loeblab/Duplex-Sequencing.
