A Sequence Distance Graph framework for genome assembly and analysis [version 1; peer review: 2 approved]

A Sequence Distance Graph framework for genome assembly and analysis [version 1; peer review: 2 approved]

Blog Article

The Sequence Distance Graph (SDG) 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 graphical fragment assembly (GFA) format.It also maps raw reads onto graphs, and provides a Python application programming interface (API) to navigate the graph, access the mapped and raw viqua-f4 data and perform interactive or scripted analyses.

Its complete workspace can be dumped to and loaded from disk, decoupling mapping from footjoy weste herren analysis and supporting multi-stage pipelines.We present the design and implementation of the framework, and example analyses scaffolding a short read graph with long reads, and navigating paths in a heterozygous graph for a simulated parent-offspring trio dataset.SDG is freely available under the MIT license at https://github.

com/bioinfologics/sdg.