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

ABSTRACT: 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

SUBMITTER: Stock W 

PROVIDER: S-EPMC11647271 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature