Qualitative comparison of the tools for pairs extraction from 3C+ sequencing data.

We consider methods modular if they have multiple tools that can be used separately or combined in a custom order. HiCExplorer is modular, but its tool for contact extraction is not (indicated with *). We consider methods flexible if they allow parameterization of data processing (e.g., restriction enzyme). We do not consider control only over technical parameters, like the number of cores, to be flexible. For restriction sites, we consider whether a method can either annotate or filter by restriction site.