{"paper":{"title":"PPanGGOLiN V2: technical enhancement and extended functionalities for prokaryotic pangenome analysis","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.GN"],"primary_cat":"q-bio.QM","authors_text":"A. Calteau (LABGeM), Adelme Bazin (LBMC UMR 5239), David Vallenet (LABGeM), Guillaume Gautreau (MaIAGE), Jean Mainguy (LABGeM), J{\\'e}r{\\^o}me Arnoux (LABGeM), T{\\'e}o Lemane (LABGeM)","submitted_at":"2026-07-27T07:50:05Z","abstract_excerpt":"The exponential growth of genomic data, particularly for microbes, has made pangenomic approaches a gold standard for large-scale comparative genomics. By capturing the full genomic diversity of a species rather than relying on a single reference, pangenomics has transformed microbial genomics, revealing the adaptive potential of bacteria and the evolutionary dynamics underlying functional diversity. Among available tools, PPanGGOLiN distinguishes itself through its graph-based model coupled with statistical gene partitioning.  Here we present PPanGGOLiN v2, which introduces substantial improv"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.24111","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2607.24111/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}