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Chromatin ligation followed by sequencing is the bedrock underlying methods for analyzing genomic architecture, but getting from short sequence reads that represent DNA segments in close physical proximity to a 3D chromatin structure requires complex computational analysis. Erez Lieberman Aiden and colleagues now present two pipelines for automated analysis. Juicer converts sequence reads into contact maps at different resolutions. It normalizes for contact probability and annotates features such as loops and contact domains. Juicebox lets a user visualize the data and zoom in and out to explore regions of interest and view them in the context of transcription and epigenetic marks.