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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Updated: Jul 1, 2026

Nanopore DNA Sequencing for Metagenomic Soil Analysis
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NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

Luke B Jones1, Stefan Bagby2

  • 1Department of Life Sciences, University of Bath, Bath, UK.

BMC Bioinformatics
|June 29, 2026
PubMed
Summary

We developed the Nanopore sequencing-based Amplicon Pipeline (NAP) for microbiome analysis. NAP offers a robust and flexible workflow for cross-domain ribosomal RNA profiling, improving taxonomic accuracy at the genus level.

Keywords:
515Y/926RAmplicon sequencingMicrobiomeNanopore sequencingRibosomal RNATaxonomic classification

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Last Updated: Jul 1, 2026

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07:33

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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Nanopore sequencing presents a portable and cost-effective method for microbiome analysis.
  • Existing amplicon-based methods face challenges with high error rates and lack of tailored workflows for mixed-domain ribosomal RNA profiling.
  • Short-read technologies, while dominant, are limited in portability and flexibility for microbial community analysis.

Purpose of the Study:

  • To introduce a robust bioinformatics pipeline specifically designed for cross-domain Nanopore amplicon data.
  • To address the limitations of existing workflows in handling mixed-domain ribosomal RNA profiling.
  • To provide a flexible and accurate tool for microbiome analysis using Nanopore sequencing.

Main Methods:

  • Developed the Nanopore sequencing-based Amplicon Pipeline (NAP), an open-source workflow.
  • Integrated dynamic quality filtering, base muting, chimera removal, and BLAST-based taxonomic classification.
  • Implemented hierarchical consensus correction, read reassignment, and blank-informed decontamination for domain-aware post-processing.

Main Results:

  • NAP demonstrated strong performance at the genus level, with reliable recovery above 1% relative abundance.
  • The consensus step significantly reduced false positive rates (82.9% at genus level, 78.8% at species level).
  • NAP outperformed QIIME2 and Kraken2/Bracken in preserving expected community structure and reducing unexpected genera.

Conclusions:

  • NAP offers a reproducible, flexible, and domain-aware consensus workflow for Nanopore amplicon profiling.
  • The pipeline shows strongest support at the genus level and competitive species-level performance for well-resolved taxa.
  • NAP enhances the utility of Nanopore sequencing for comprehensive microbiome analysis.