Nanopore FAQs

If you would like to submit your DNA through one of our services, even though the recommendations have not been met, it is still possible that the sample would sequence at a reduced concentration, however we cannot guarantee this.

If you cannot meet the recommended requirements, please let us know by leaving us a note when placing an order, confirming the amount of DNA you have been able to generate. Please note by not sending your DNA at the requirements you may not get the quality and read length you were expecting, we do not offer repeats or refunds for failed sequencing if the sample does not meet our recommendations.

By using our pre-treatment RCA on your samples, you can:

Increase sequencing quality and depth particularly in low-yield plasmid samples, we provide RCA as an optional enhancement. RCA is a highly efficient method that amplifies and enriches circular DNA to produce clean, high-coverage input for nanopore sequencing.

• Bacterial cultures can be submitted directly, eliminating the need for DNA extraction
• Generate long, overlapping reads that assist with assembly
• Maximise data output from samples with limited DNA concentration

By using our colony PCR pre-treatment on your samples, you can:

Target a loci for amplification using selected primers. This can deliver clean, high-quality sequencing data direct from bacterial colonies or liquid cultures, supporting a range of applications from plasmid verification to high-throughput mutant screening.

Service features include:

• Direct amplification from cultures or gDNA: Samples are accepted in 96-well plate format using 150 µL of glycerol-free overnight culture or extracted genomic DNA.
• Validated or custom primer use: Submit your own primers or select from our free library of over 40 validated options for amplification.
• Purification of PCR products: Amplified DNA is cleaned to remove contaminants, ensuring compatibility with downstream sequencing.
• Enhanced chemistry for complex templates: Optional treatment improves results for GC-rich or structurally challenging sequences.
• Trusted across disciplines, including molecular biology, synthetic biology, and biotechnology, researchers rely on us for consistent data quality, rapid sequencing, and expert support that simplifies every stage of validation.

Nanopore plasmid:

If a reference sequence is submitted for plasmid/BAC analysis a QC report comparing the de novo assembly to the reference provided. The reference is not used in the construct assembly.

Nanopore30- For rapid sequencing and assembly of plasmids up to 30kb.

Nanopore150- For sequencing and assembly of plasmids/BACs up to 150kb.

Nanopore300- For sequencing and assembly of plasmids/BACs up to 300kb.

Nanopore Amplicon:

Can be used to analyse specific target regions of DNA. Our Amplicon sequencing has two pathways de novo assembly and variant call analysis are both available. The default analysis is de novo report which assembles a single consensus sequence with each sample. If a reference Is provided a variant call analysis is conducted which is the comparison of the sequence to the reference file submitted.

Automatically receive raw reads:

This option includes a FASTQ file for each sample containing the reads that align to either your assembled amplicon or any of the included reference sequences provided with the order.

Plasmid extraction:

Requires a submission of 1 ml of overnight culture which we then extract and process through our nanopore30, 150 or 300 services. Our plasmid extraction service is a SPRI paramagnetic bead-based system which can be used to purify a variety of high- and low-copy number template types. It is a high throughput service performed on an automated workstation, so the total plasmid prep time is much quicker than a manual kit.

Rolling circle amplification (RCA):

Submission of around 50μl of overnight culture, which we amplify and the process through nanopore 30, 150 or 300. RCA can increase sequencing quality and consistency, particularly in low-yield plasmid samples, we provide RCA as an optional enhancement. RCA is a highly efficient method that selectively amplifies circular DNA to produce clean, high coverage input for nanopore sequencing. Customers can submit bacterial cultures directly, eliminating the need for DNA extraction.

Colony:

Submissions of 150μL of Overnight Culture - glycerol free where possible, supplied in a 96 well plate, or extracted gDNA. Please note a forward and reverse primer will be needed and selected on the website when ordering. Primers can be our own house primers, provided by customer at 10 pmol/μl in a volume of 100 μl per primer or synthesised which will be stored in our lab for a year (Please note that synthesising primers can take 2-3 days).

Colony targets loci for amplification using selected primers. This can deliver clean, high-quality sequencing data directly from bacterial colonies or liquid cultures, supporting a range of applications from plasmid verification to high-throughput mutant screening.

Please clearly label your samples with the names you have submitted online. Failure to do this may result in delays to your turn around time. When submitting to us please clearly state the order number on your envelope, the order number is displayed at the point the order is successfully placed.

If you have less than 48 samples, please send them clearly labelled in either PCR strip tubes or each individual sample in single eppendorf tubes.

If you have more than 48 samples, we would recommend sending them in a 96 well plate, sealed well with an adhesive foil seal to prevent leaking.

Delivering unrivalled turnaround times for Whole Plasmid Nanopore Sequencing using our streamlined SpeedREAD™ data delivery system. Providing high-quality data retrieval within 12 hours* from sample receipt.

If you have selected a Pre-treatment for your sample the data retrieval could be higher between 12- 24 hours from sample receipt.

*May vary depending on your exact requirements. Contact us in case of any questions. 10 hours or less from sample receipt to results in the vast majority of cases.

For our analysis software the target output is a single consensus sequence. You can send mixtures of plasmids at your own risk, but this may not get the clear data reads you need. We will return a single consensus sequence for the plasmid which produces the largest amounts of sequencing data. If your sample is expected to contain constructs that only slightly vary from a provided reference sequence, you should opt for the raw reads option and may be able to identify the variation with your own bioinformatic analysis.

All the Nanopore services and pre-treatments can be ordered using our E-Vouchers, these can be purchased through the portal in various quantities and then used as required.

You are also able to use credit card or a Purchase Order number to complete the payment if preferred.

One of the easiest ways to obtain a quote for the Nanopore services is to visit our Sequencing Portal https://genomics.sourcebioscience.com/ and add the required options you wish to order into your basket. You can then generate a quote containing your basket contents, downloadable direct from the portal.

If you have any questions or would like a bespoke quote for a larger order, please contact our Sales team by email GSTeam@sourcebioscience.com.