Animal sequencing

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. Long nanopore sequencing reads (>4 Mb achieved), provide novel and cost-effective insights into animal genomes, transcriptomes, and microbiomes, through the accurate resolution of complex genomic regions, haplotypes, and full-length transcripts. Direct sequencing of native DNA or RNA further allows simultaneous identification of base modifications (e.g. methylation) alongside nucleotide sequence.

Using a single sequencing technology without parental data, this QV score [QV 31.3] approaches the ‘platinum-quality’ reference genome standard of Q40 (99.99% accuracy)...

Flack, N. et al. NAR Genom. Bioinform. 5(2), lqad033 (2023).

Technology comparison

Oxford Nanopore sequencing

Traditional short-read technologies

Unrestricted read length (>4 Mb achieved)

Read length typically 50–300 bp

Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform identification.

Direct, amplification-free protocols

  • Detect base modifications as standard — no additional prep required
  • Eliminate amplification bias, GC-bias, and read length limitations
  • Perform target enrichment without additional wet-lab prep using adaptive sampling

Amplification required

Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications (e.g. methylation), necessitating additional sample prep, sequencing runs, and expense.

Flexible and on-demand

  • Scale to your throughput needs
  • Sequence in the lab or field with portable Flongle and MinION
  • Tackle large animal genome projects with flexible, high-output GridION and PromethION devices
  • No sample batching required

Limited flexibility

Platform costs and infrastructure requirements can limit global accessibility, with no facility for sequencing samples in the field. Sample batching may also be required for optimal efficiency, potentially delaying results.

Real-time data streaming

  • Get immediate access to results for time critical applications such as pathogen identification
  • Enrich targeted regions based on real-time sequence composition using adaptive sampling
  • Stop sequencing when sufficient data generated — wash and reuse flow cell
  • Use intuitive EPI2ME data analysis workflows

Fixed run time with bulk data delivery

Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.

Streamlined workflows

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.

White papers

New insights into large genomes

From delineating complex genomic regions, such as repeats and structural variants, to simultaneous calling of methylated bases alongside nucleotide sequence, discover how nanopore sequencing is being used to generate enhanced, highly-contiguous animal genome assemblies. Specific case studies reveal how researchers are applying the benefits of long, real-time nanopore sequencing reads to a wide range of research areas, including solving a chromosome conundrum in the creeping vole that had puzzled researchers for over 60 years.

Interested in animal genome assembly? Read our end-to-end workflow for best practice guidance — from DNA extraction through to sequencing and analysis.

Get more animal sequencing content, including getting started guides, workflows, and videos, in our Resource centre.

Case study

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

The kākāpō parrot is a nocturnal, flightless bird endemic to New Zealand with a population of just 252. To support conservation of this critically endangered species, researchers at the University of Otago, New Zealand, developed an environmental DNA (eDNA) metabarcoding approach using the portable MinION device to non-invasively monitor the kākāpō population. The combination of long nanopore sequencing reads with adaptive sampling — Oxford Nanopore’s unique on-device target enrichment methodology — enabled the team to identify individual birds, potentially expanding the application of real-time eDNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.

This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species...

Urban, L. et al. eLife12:RP84553 (2023).

Case study

Using nanopore ultra-long reads for highly accurate telomere-to-telomere assembly of the tammar wallaby genome

At the NCM2022, Patrick Grady (University of Connecticut, USA) presented his work using nanopore sequencing to create complete and phased telomere-to-telomere genome assemblies and epigenetic profiles for the tammar wallaby, Macropus eugenii. The new assemblies provided a significant improvement to the currently available genome data for this model organism and will provide insights into mammalian evolution.

Get started

Scalable sequencing for animal research

From powerful, portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION devices — scale your sequencing to match your specific research requirements.

Recommended for animal genomics

PromethION 24

Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of sequencing data — ideal for cost-effective, high-throughput sequencing of animal genomes, large animal genome sequencing projects, transcript-based genome annotation, and isoform-level transcriptomics.


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