ODGI: understanding pangenome graphs

Motivation: Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way. Results: We wrote ODGI, a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA variation graphs. ODGI includes tools for detecting complex regions, extracting loci, removing artifacts, exploratory analysis, manipulation, validation, and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs. Availability: ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io. ODGI can be installed via Bioconda https: //bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/ ekg/guix-genomics/blob/master/odgi.scm.