Panacus: fast and exact pangenome growth and core size estimation

Abstract

AbstractMotivationUsing a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (thecore genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).ResultsWe introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in less than one hour.AvailabilityPanacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available athttps://github.com/marschall-lab/panacus. Panacus can be installed via Bioconda athttps://bioconda.github.io/recipes/panacus/README.html.ContactLuca Parmigiani (luca.parmigiani@uni-bielefeld.de), Daniel Doerr (daniel.doerr@hhu.de).