Pannagram: unbiased pangenome alignment and the Mobilome calling

Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple genome alignment in different modes, extracting features such as structural variants (SVs), and searching sequences between datasets; and an R library that provides tools for analyzing alignments and SVs, as well as visualizing every step of the Mobilome analysis pipeline. As a proof of concept, we applied Pannagram to 12 Cucumis sativus genomes, identified SVs, and constructed the graph of nestedness for these variants. Within this graph, we identified families of actually mobile elements belonging to known transposable element families (LINEs, LTRs, and TIRs) and uncovered candidates for a novel type of mobile elements. Our results highlight the power of Pannagram in Mobilome discovery while ensuring an unbiased approach to pangenome analysis.