Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

Vertaalde titel van de bijdrage: Referentieloos: referenties: een consensus benadering voor gemeenschapsprofilering met lange amplicon nanopore-data

Willem Stock, Coralie Rousseau, Glen Dierickx, Sofie D’hondt, Luz Amadei Martínez, Simon M. Dittami, Luna M. van der Loos, Olivier De Clerck

Onderzoeksoutput: Bijdrage aan tijdschriftA1: Web of Science-artikelpeer review

Uittreksel

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).
Vertaalde titel van de bijdrageReferentieloos: referenties: een consensus benadering voor gemeenschapsprofilering met lange amplicon nanopore-data
Oorspronkelijke taalEngels
Artikel nummerbbae642
Volume26
Exemplaarnummer1
Pagina's (van-tot)1
Aantal pagina’s10
ISSN1477-4054
DOI's
PublicatiestatusGepubliceerd - 16-dec.-2024

Thematische Lijst 2020

  • Andere

Technologisch

  • genetische technieken

Vrije trefwoorden

  • nanopore

Dit citeren