ArticleBriefings in bioinformatics2024
Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Illuminating the "black boxes" of microbiome sequencing.Journal of microbiology & biology education · 2026Article
- Soil microbial diversity, succession, and greenhouse gas cycling across a Greenlandic glacial chronosequence.FEMS microbiology ecology · 2026Article
- Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short- and Long-Read Approaches.Ecology and evolution · 2026Article
- Detecting foldback artifacts in long-reads.BMC genomics · 2026Article
- Detecting Foldback Artifacts in Long-reads.bioRxiv : the preprint server for biology · 2025Article
- Barcode sequencing: a robust, platform-agnostic method for massively parallel cell-based screens.G3 (Bethesda, Md.) · 2025Article
- What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in DecayingJournal of fungi (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
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, 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).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.