Animal research with nanopore sequencing technology
Animal genomics provides valuable insights into many scientific research areas — from the use of model organisms to study human disease, through to animal health, breeding, conservation, and evolution. A shared challenge across all of these disciplines is the requirement for accurate characterisation of large and highly complex genomic regions. Using long nanopore sequencing reads (up to 2 Mb), researchers are now able to resolve structural variants, repetitive regions, haplotypes, and full-length transcripts, providing novel insights into animal genomes, transcriptomes, and microbiomes. Further, the facility to directly sequence native DNA and RNA allows streamlined identification of base modifications alongside the nucleotide sequence.
- Resolve challenging genomic regions such as structural variants and repeats using long reads
- Sequence full-length RNA transcripts in single reads for unambiguous isoform identification and quantification
- Detect base modifications as standard alongside nucleotide sequence
- Streamline your workflow with 10-minute library prep
- Accessible to any laboratory — scale using Flongle, MinION, GridION, or PromethION
- Real-time results for time-critical applications such as pathogen identification
How will you use nanopore technology?
Whole genome sequencing
Pathogens & microbiota
Correct and complete genome assemblies of model and non-model organisms using long nanopore sequencing reads. Fully characterise complex structural variants, repeat regions, and phasing to support breeding programmes and evolutionary analysis. Gain new insights into animal health and disease.
- Obtain complete genomes and correct reference assemblies with de novo or reference guided approaches
- Accurately resolve structural variants, repeat regions, and phasing
- Detect epigenetic modifications using direct sequencing — and eliminate PCR bias
- Streamline your workflow with rapid, 10-minute library prep and real-time analysis
- Scale to your requirements — 1.8 Gb Flongle; 30 Gb MinION; 150 Gb GridION;
‘The long-read chemistry generated by [Oxford Nanopore] was useful for addressing challenges related to de novo assembly, particularly at regions containing repetitive sequences spanning longer than the read length, and which could not be resolved with only short-read–based assembly’
Dhar et al
Unraveling shark secrets: sequencing genomes and microbiomes for research and conservation
Move beyond standard SNV analysis of short targeted regions. Long nanopore sequencing reads allow cost-effective detection and phasing of all variant types — including structural variants, repeats, microsatellites, and SNVs — across large genomic regions of interest. Simultaneously analyse base modifications alongside nucleotide sequence using PCR-free enrichment methods. Match your coverage and throughput requirements to our scalable technology and utilise sample multiplexing for even more cost-effective analyses.
- Resolve and phase all genetic variation across large genomic regions — including structural variants, repeats, microsatellites, and SNVs
- Analyse entire genes, including exons, introns, and promoters in single reads
- Your choice of enrichment strategy — PCR, hybrid-capture,CRISPR/Cas9
- Detect epigenetic modifications using amplification free-enrichment and sequencing
- Don’t wait for results — analyse data in real time
- Multiplex samples for even more cost-effective results
‘MinION sequencing is rather inexpensive and faster than most established DNA sequencing methods, and the throughput is particularly suitable for amplicon experiments’
Fuselli et al
Field-forward sequencing with Oxford Nanopore technology: a strategy to establish the upside-down mangrove jellyfish Cassiopea xamachana as a bioindicator
Nanopore sequencing delivers high yields of long, full-length reads, allowing unambiguous characterisation and quantification of transcript isoforms. Unlike traditional RNA-seq techniques, no amplification is required — removing sources of bias and enabling direct detection of base modifications alongside nucleotide sequence. Low input amounts combined with rapid, streamlined workflows enable highly sensitive gene expression analysis.
- Sequence full-length transcripts for unambiguous identification of splice variants
- High yields enable transcript quantification and gene expression analysis
- Eliminate PCR bias using direct cDNA or direct RNA sequencing
- Detect base modifications alongside nucleotide sequence using direct sequencing
- Use targeted approaches to analyse specific transcripts of interest
- Get higher yields from less input using the latest RNA and cDNA sequencing kits
‘To provide an accurate isoform-level transcriptome annotation for non-model organisms, long-read sequencing technology is required to sequence full-length cDNA molecules’.
Byrne et al
Depletion of abundant transcripts using cas-9 and long-read sequencing improves transcriptome annotation of the polar bear
Direct nanopore sequencing does not require amplification, strand synthesis, or bisulfite conversion, reducing bias and allowing detection of modified DNA or RNA bases alongside the nucleotide sequence. Base modifications can be detected using PCR-free whole genome, whole transcriptome, and targeted sequencing approaches.
- Cost-effectively identify modified bases and nucleotide sequence
- Capture base modifications as standard — analyse when you are ready
- Rapid 10-minute library prep — no bisulfite conversion required
- Phase modified bases using long reads
- Analyse data using Tombo, one of a growing number of tools
'The establishment of the [Oxford Nanopore] platform as a tool to map virtually any given modification will allow us to query the epitranscriptome in ways that, until now, had not been possible'
Liu et al
Targeted nanopore sequencing with Cas9 for studies of methylation, structural variants and mutations
Real-time, long-read nanopore sequencing allows rapid and comprehensive characterisation of animal pathogens and microbiota, supporting improvements in animal health and welfare, reducing antibiotic usage, and enhancing outbreak surveillance. Samples can be sequenced at source or in the lab using the portable Flongle and MinION devices or benchtop GridION X5 or PromethION platforms. Real-time results deliver immediate and actionable insights.
- Identify microbes and antimicrobial resistance in real-time
- Differentiate closely related strains using long reads
- Streamline your workflow with rapid whole genome or targeted (e.g. 16S) approaches
- Sequence samples at 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;
'We detected the first viral reads just 7 seconds after the start of sequencing'
Dr. Sebastiaan Theuns, Ghent University
Going full circle: Assembly of high-quality, single-contig microbial genomes from the rumen microbiome using long-read sequencing