Animal sequencing
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'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. (2023)
Novel insights into animal genomes and transcriptomes
Animal genomics provides valuable insights into many scientific research areas — from the use of model organisms to the study of human diseases, through to animal health, breeding, conservation, and evolution. Nanopore sequencing reads of unrestricted length, from short to ultra long, 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. Furthermore, direct sequencing of native DNA or RNA further allows simultaneous identification of epigenetic modifications (e.g. methylation) alongside nucleotide sequences.
Featured content
Advances in Oxford Nanopore read accuracy
This poster describes how to achieve accurate and complete assemblies for genomes of any size across a wide variety of organisms, including honeybee (Apis mellifera) and zebu cattle (Bos indicus), using highly scalable telomere-to-telomere (T2T) assembly workflows.
ORG.one to 10
Hear from Heather Ritchie-Parker, a Research Scientist at the Royal Zoological Society of Scotland, and Ben, a Principal Curator at the Natural History Museum, London, about ORG.one during a Showcase session at London Calling.
Recommended device for animal genomics
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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.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
