The Sequence Distance Graph framework works with genome assembly graphs and raw data from paired, linked and long reads. It includes a simple deBruijn graph module, and can import graphs using the GFA format. It also maps raw reads onto graphs, and provides a Python API to navigate the graph, access the mapped and raw data and perform interactive or scripted analyses. Its complete workspace can be dumped to and loaded from disk, decoupling mapping from analysis and supporting multi-stage pipelines.

This work was strategically funded by the BBSRC Core Strategic Programme Grant (BBS/E/T/000PR9818). Work by GGA and BJC was also partially funded by the BBSRC grant "OctoSeq: Sequencing the octoploid strawberry" (BB/N009819/1).