{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T12:10:41Z","timestamp":1773058241600,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,16]],"date-time":"2024-12-16T00:00:00Z","timestamp":1734307200000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["1252821"],"award-info":[{"award-number":["1252821"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["3F020119"],"award-info":[{"award-number":["3F020119"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biodiversa+ RESTORESEAS","award":["G0G3921N"],"award-info":[{"award-number":["G0G3921N"]}]},{"name":"EMBRC Belgium - FWO project","award":["GOH3817N"],"award-info":[{"award-number":["GOH3817N"]}]},{"name":"EMBRC Belgium - FWO project","award":["I001621N"],"award-info":[{"award-number":["I001621N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterize communities through the sequencing of long amplicons. While this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic for accurately identifying the community members present within a sample. Here, we present and validate CONCOMPRA, a tool that allows the detection of closely related strains within a community by drafting and mapping to consensus sequences. We show that CONCOMPRA outperforms several other tools for profiling bacterial communities using full-length 16S rRNA gene sequencing. Since CONCOMPRA does not rely on a sequence database for profiling communities, it is applicable to systems and amplicons for which little to no reference data exists. Our validation test shows that the amplification of long PCR products is likely to produce chimeric byproducts that inflate alpha diversity and skew community structure, stressing the importance of chimera detection. CONCOMPRA is available on GitHub (https:\/\/github.com\/willem-stock\/CONCOMPRA).<\/jats:p>","DOI":"10.1093\/bib\/bbae642","type":"journal-article","created":{"date-parts":[[2024,12,16]],"date-time":"2024-12-16T10:34:41Z","timestamp":1734345281000},"source":"Crossref","is-referenced-by-count":9,"title":["Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7648-6404","authenticated-orcid":false,"given":"Willem","family":"Stock","sequence":"first","affiliation":[{"name":"Phycology Research Group, Ghent University , 9000 Gent,","place":["Belgium"]}]},{"given":"Coralie","family":"Rousseau","sequence":"additional","affiliation":[{"name":"Sorbonne University, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M, UMR 8227), Station Biologique de Roscoff (SBR), Roscoff ,","place":["France"]}]},{"given":"Glen","family":"Dierickx","sequence":"additional","affiliation":[{"name":"Research Group Mycology, Ghent university , 9000 Gent,","place":["Belgium"]},{"name":"Research Unit Forest Ecology and Management, Research Institute for Nature and Forest , Geraardsbergen,","place":["Belgium"]}]},{"given":"Sofie","family":"D'hondt","sequence":"additional","affiliation":[{"name":"Phycology Research Group, Ghent University , 9000 Gent,","place":["Belgium"]}]},{"given":"Luz","family":"Amadei Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Laboratory of Protistology and Aquatic Ecology, Ghent University , 9000 Gent,","place":["Belgium"]}]},{"given":"Simon M","family":"Dittami","sequence":"additional","affiliation":[{"name":"Sorbonne University, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M, UMR 8227), Station Biologique de Roscoff (SBR), Roscoff ,","place":["France"]}]},{"given":"Luna M","family":"van der Loos","sequence":"additional","affiliation":[{"name":"Phycology Research Group, Ghent University , 9000 Gent,","place":["Belgium"]}]},{"given":"Olivier","family":"De Clerck","sequence":"additional","affiliation":[{"name":"Phycology Research Group, Ghent University , 9000 Gent,","place":["Belgium"]}]}],"member":"286","published-online":{"date-parts":[[2024,12,16]]},"reference":[{"key":"2024121610342999600_ref1","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1093\/biomethods\/bpaa026","article-title":"Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples","volume":"6","author":"D\u2019Andreano","year":"2021","journal-title":"Biol Methods Protoc"},{"key":"2024121610342999600_ref2","doi-asserted-by":"publisher","first-page":"102456","DOI":"10.1016\/j.algal.2021.102456","article-title":"Characterizing algal microbiomes using long-read nanopore 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