Frequently Asked Questions - Nanopore Sequencing

Oxford Nanopore Technologies (ONT) sequencing generates long reads that can span repetitive or complex regions. This makes it particularly useful for plasmid verification, microbial genome assembly, structural variant analysis and long amplicon sequencing. Suitable workflows can also detect modifications in native DNA.

Microsynth offers standardized ONT services and customized solutions for specific sequencing or bioinformatics requirements.

ONT is particularly useful when your question depends on long, continuous sequences, for example when resolving repeats or analyzing complete plasmids. Illumina is often suitable for applications requiring large numbers of short reads, while Sanger is a practical option for checking individual short sequence regions.

The best choice depends on your target, sample number and required analysis. We can help you select the appropriate approach.

Choose the service that matches your sample and research question:

• Full PlasmidSeq: plasmid and other supported circular or linear DNA sequencing.
• Long PCRSeq: consensus sequencing of long PCR products. The current standard service does not analyze sequence diversity within a sample.
• BacterialSeq: bacterial genome sequencing.
• YeastSeq: yeast genome sequencing.
• nanoCORE Amplicon Metagenomics: microbial community analysis using full-length marker gene amplicons.

Projects outside these standard workflows can be evaluated as customized ONT projects. Send us your sample type, sample number, expected genome or target size, and study objective for advice.

For genomic long-read sequencing, intact, high molecular weight DNA with minimal fragmentation is generally preferred. DNA integrity influences the read lengths that can be obtained and the ability to span complex regions during assembly.

Requirements differ for genomic DNA, plasmids and PCR products. When submitting PCR products, follow the requirements for the intended amplicon rather than those for high molecular weight genomic DNA. Follow the concentration, quantity, purity and fragment size requirements in the user guide for your selected service.

For selected services, Microsynth offers DNA preparation or isolation from supported starting materials. Accepted sample types and any additional charges depend on the service.

Check the relevant service page and user guide before submitting cultures or other biological material. For customized projects, contact us before shipment to confirm sample acceptance, preparation and shipping requirements.

The coverage required depends on your application, sample complexity and analysis objective. The total amount of sequencing data needed to achieve that coverage also depends on the genome or target size. Standardized services have predefined specifications. For customized projects, we can help define an appropriate data volume, read number or target coverage.

Please indicate whether your goal is an assembly, reference comparison, variant detection or another analysis, as these may require different coverage levels.

Accuracy depends on the sequencing workflow, data quality and analysis method. The accuracy of an individual read differs from that of a consensus sequence or genome assembly, which combines information from multiple reads.

The relevant performance criteria therefore depend on your application. If your project requires detection of specific sequence changes or low-frequency variants, discuss these requirements with us before ordering.

A reference sequence is not required for de novo assembly, where sequences are reconstructed from the sequencing reads. A reference is useful for checking an expected construct or identifying differences from a known sequence.

If you have a reference, please provide it with your order and explain what you would like to compare. The required reference information depends on the selected service and analysis.

Yes. Purified PCR products can be evaluated for customized ONT sequencing when the standard services do not fit your application.

Please provide the amplicon length, number of samples, whether each sample contains one amplicon or a mixture, expected sequence diversity, required read number and analysis objective. These details help us select a suitable library preparation and sequencing strategy.

Deliverables depend on the service and bioinformatics package. Typical formats used for ONT results include FASTQ for sequencing reads and FASTA for assembled or consensus sequences. Depending on the project, results may also include annotation files, variant results, taxonomic profiles or an analysis report.

The files included in your order are defined by the service specification or quotation. If you require a specific data format, please discuss this with us before ordering.

Yes. Standardized services include defined analysis pipelines. Depending on the service, analyses may include de novo genome assembly, genome annotation, variant analysis or taxonomic profiling.

Customized analyses are evaluated according to your research question and the available data and reference information. Please describe the biological result you need when requesting a quotation.

Yes, suitable ONT workflows can detect certain DNA modifications directly from native DNA. This requires an appropriate PCR-free preparation and a compatible analysis model. Standard PCR amplification does not preserve the original DNA methylation pattern.

Modification analysis is not automatically included in every ONT service. If methylation or another base modification is a project objective, contact us before ordering so we can assess feasibility and define the sequencing and analysis setup.

Turnaround times depend on the service, starting material, sample number and analysis scope. Check the relevant service page for standard turnaround times. For customized projects, the expected timeline is agreed during quotation.

Please also allow for shipping and, where applicable, transfer to the processing laboratory. If you have a deadline, discuss it with us before submitting your samples.

Yes. If a standard service does not fit your application, Microsynth can assess a customized solution.

For a quotation, please provide the sample number and type, starting material, expected genome or target size, study objective, and any required sequencing depth, read number or bioinformatics analysis. Also mention available reference sequences, required file formats and your preferred timeline