{"paper":{"title":"On the representation of de Bruijn graphs","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.DS","q-bio.GN"],"primary_cat":"q-bio.QM","authors_text":"Antoine Limasset, Jared Simpson, Paul Medvedev, Rayan Chikhi, Shaun Jackman","submitted_at":"2014-01-21T16:55:02Z","abstract_excerpt":"The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers proposed a navigational data structure approach in order to improve memory usage. We prove several theoretical space lower bounds to show the limitation of these types of approaches. We further design and implement a general data structure (DBGFM) and demonstrate its use on a human whole-genome dataset, achieving space usage of 1.5 GB and a 46% improvement over "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1401.5383","kind":"arxiv","version":4},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"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"}