Resources Get started
Home > Applications > Microbiology

Microbiology using nanopore sequencing technology

Complete bacterial, fungal, and viral (DNA or RNA) genomes with long-read nanopore sequencing. Identify and characterise microbes from environmental or single organism samples, with rapid methods for pathogen detection — whether at the bench or in the field. Accompanied, if required, with antimicrobial resistance profiling. Sequence full-length transcripts using direct RNA or cDNA methods for accurate gene expression and transcript isoform analysis.

  • Simplify de novo assembly and correct reference genomes with long and ultra-long reads
  • Resolve structural variation and repetitive regions
  • Sequence and quantify full-length transcripts for unambiguous gene expression and isoform analysis
  • Eliminate bias and identify epigenetic modifications with direct sequencing
  • Get results, including species identification, in real time
  • Scale to your needs using Flongle, MinION, GridION, or PromethION

How will you use nanopore technology?

Genome analysis

Species ID & AMR profiling



Get comprehensive analysis of microbial genomes (DNA or RNA). Accurately map repetitive regions and structural variants, and differentiate plasmid from genome using long sequencing reads. Simplify de novo assembly and correct existing reference genomes. Scale to suit your needs from bench to the field.

Based on current internal flow cell performance of 200 Gb (October 2018).

  • Accurately resolve challenging genomic regions (structural variants and repeats) 
  • Simplify de novo assembly and correct reference genomes with long reads
  • Use whole genome, targeted, and multiplexing approaches
  • Eliminate bias with PCR-free, direct DNA and RNA sequencing
  • Get immediate results with real-time data streaming
  • Scale to suit your needs — 1.8 Gb Flongle; 30 Gb MinION; 150 Gb GridION; 4,800/9,600 Gb PromethION P24/P48

'Importantly, we demonstrate that a single MinION run based on a straightforward 10-minute library preparation protocol allows a 67-fold increase in genome contiguity and improves genome completeness by 28% when compared with short-read-only assemblies' 

Díaz-Viraqué et al

Ami Bhatt: Closing highly repetitive bacterial genomes from metagenomic nanopore sequencing

Accurately identify microorganisms and associated antimicrobial resistance (AMR) in real time. Oxford Nanopore offers a complete solution — from rapid, 10-minute library prep (DNA), to real-time phylogenetic and AMR analysis using the EPI2ME platform. Use metagenomic or targeted 16S rRNA approaches. Sequence at sample source or in the lab using the portable MinION or benchtop GridION X5 or PromethION devices.

  • Identify microbes and AMR in real-time and differentiate closely related strains using long reads
  • Streamline your workflow with rapid whole genome or targeted (e.g. 16S) approaches
  • Sequence at sample source using the portable MinION and Flongle
  • Multiplex samples for even more cost-effective results
  • Scale to suit your needs — 1.8 Gb Flongle; 30 Gb MinION; 150 Gb GridION; 4,800/9,600 Gb PromethION P24/P48

Resolve transcript isoforms and measure true gene expression profiles using full-length nanopore sequencing reads. Low input amounts combined with rapid, streamlined workflows enable highly sensitive gene expression analysis

  • Sequence entire, full-length transcripts for unambiguous identification of transcript isoforms
  • Accurately quantify isoforms for sensitive gene expression analysis
  • Eliminate PCR bias using direct cDNA or direct RNA sequencing
  • Easily identify anti-sense transcripts and lncRNA isoforms
  • New: Get higher yields from less input using updated RNA and cDNA sequencing kits

Microorganisms exhibit many types of base modification that can influence a range of functions, including gene expression and antimicrobial resistance. Unlike alternative sequencing-based analysis approaches, nanopore sequencing does not require amplification or strand synthesis, reducing bias and preserving modified base information, which can be directly detected alongside the nucleotide sequence – with no requirement for additional sample conversion. 

  • Identify modified bases and nucleotide sequence in a single assay
  • Capture base modifications as standard – analyse when you are ready
  • Use PCR-free whole genome, whole transcriptome or targeted sequencing approaches
  • Explore genome replication using nucleotide analogues
  • Rapid 10-minute library prep (DNA) – no bisulfite or chemical conversion required
  • Analyse data using a growing number of tools
Open a chat to talk to our sales team