{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T11:07:06Z","timestamp":1784027226122,"version":"3.55.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2020,7,16]],"date-time":"2020-07-16T00:00:00Z","timestamp":1594857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01HG010961"],"award-info":[{"award-number":["U01HG010961"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U41HG010972"],"award-info":[{"award-number":["U41HG010972"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG010485"],"award-info":[{"award-number":["R01HG010485"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["2U41HG007234"],"award-info":[{"award-number":["2U41HG007234"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5U54HG007990"],"award-info":[{"award-number":["5U54HG007990"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5T32HG008345-04"],"award-info":[{"award-number":["5T32HG008345-04"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01HL137183"],"award-info":[{"award-number":["U01HL137183"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000888","name":"W. M. Keck Foundation","doi-asserted-by":"publisher","award":["DT06172015"],"award-info":[{"award-number":["DT06172015"]}],"id":[{"id":"10.13039\/100000888","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Central Innovation Programme"},{"name":"Federal Ministry for Economic Affairs and Energy of Germany"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic datasets can be challenging to work at. These challenges have impeded progress in this field.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a stack of two C++ libraries, libbdsg and libhandlegraph, which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage are up to an order of magnitude better than the prior graph implementation in the VG toolkit, which has now transitioned to using libbdsg\u2019s implementations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>libhandlegraph and libbdsg are available under an MIT License from https:\/\/github.com\/vgteam\/libhandlegraph and https:\/\/github.com\/vgteam\/libbdsg.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa640","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T11:34:24Z","timestamp":1594380864000},"page":"5139-5144","source":"Crossref","is-referenced-by-count":26,"title":["Efficient dynamic variation graphs"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8345-8356","authenticated-orcid":false,"given":"Jordan M","family":"Eizenga","sequence":"first","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5828-047X","authenticated-orcid":false,"given":"Adam M","family":"Novak","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9041-5167","authenticated-orcid":false,"given":"Emily","family":"Kobayashi","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Bioinformatics and Systems Biology, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3633-0610","authenticated-orcid":false,"given":"Flavia","family":"Villani","sequence":"additional","affiliation":[{"name":"Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy"},{"name":"Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli Federico II , Naples 80138, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8487-5936","authenticated-orcid":false,"given":"Cecilia","family":"Cisar","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3326-817X","authenticated-orcid":false,"given":"Simon","family":"Heumos","sequence":"additional","affiliation":[{"name":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenn","family":"Hickey","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincenza","family":"Colonna","sequence":"additional","affiliation":[{"name":"Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedict","family":"Paten","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Garrison","sequence":"additional","affiliation":[{"name":"Genomics Institute , Santa Cruz, CA 95064, USA"},{"name":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,16]]},"reference":[{"key":"2023062408060684700_btaa640-B1","first-page":"20","article-title":"Hash tables with pseudorandom global order","volume":"18","author":"Brehm","year":"2019","journal-title":"INFOCOMP J. 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