The right answers to frequently asked questions
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How does whole plasmid sequencing compare to Sanger sequencing?
There are pros and cons of every sequencing method. Sanger sequencing and Oxford Nanopore sequencing (ONT) are both methods for determining the sequence of nucleotides in a piece of DNA. Typically Sanger is consider the most accurate method for short-read sequencing and NGS is better for long-read sequencing.
Overall, the choice between Sanger sequencing and ONT will depend on the specific needs of the application. Both methods have their strengths and limitations, and the appropriate method will depend on factors such as the length and quality of the DNA sample, the desired level of accuracy, and the cost and availability of the necessary equipment.
What is the coverage?
It really depends on the sample quality. We cannot guarantee the level of coverage at this time. A good sample submitted properly will typically yields hundreds or even thousands of sequencing reads. Consensus coverage depends on how many reads are full-length plasmids and how many, if any, degraded.
A coverage exceeding approximately 20x indicates a highly accurate consensus sequence.
Is there a minimum number of samples I must submit?
Any number of samples is welcome. There are no minimums or limitations.
Can you sequence my mixture of plasmids?
You can send it and we can sequence it, but we cannot predict or promise the analysis outcome. The customer would take on the risk of these orders.
Do you offer a prepaid solution for whole plasmid sequencing?
Great news! We are actively working on bringing you a prepaid solution, which will be available very soon!
Can I also sent amplikons and large insert DNA for the Whole Plasmid Sequencing service?
Unfortunately not. Currently, we can only accept plasmids. However, we do offer a special service for amplicons and large DNA inserts, which is available for your use. Learn more >>
Can I send my samples without the free barcode?
Unfortunately not. This barcode is required for our internal lab processes and is essential in ensuring that we can process your samples as efficiently as possible. Thank you for your cooperation!
Can I use my local dropbox to ship samples for Whole Plasmid Sequencing?
Yes of course.
If you don't know if there is a dropbox close by, use our dropbox location page to find out. Please click here >>
Will you also deliver the FASTQ data?
Yes, FASTQ files are delivered for every project.
Troubleshooting guide for failed samples
There are several reasons why your sample might have failed:
- The starting material did not consist of circular DNA.
In our library preparation protocol, circular DNA is required as the starting material. If linear DNA is provided, it will result in sample fragmentation and subsequently lead to poor or no results.
- Insufficient DNA concentration in prepared samples.
The primary reason for this issue is the use of a Nanodrop device to measure DNA concentration. We strongly recommend employing a Qubit or a similar method instead.
- Presence of mixed plasmid species and/or fragmented genomic DNA or fragmented plasmids within the samples.
You may detect signs of this failure mode through a wide range of read lengths reported in the raw read length histogram.
To interpret your results you can also have a look at our troubleshooting guide. Click here >>
Which buffer should I use to send my samples?
Please send your samples in nuclease-free water or elution buffer.
Please do not use a buffer containing EDTA.
Will you repeat sequencing of my sample if the sequencing fails?
For each run, we conduct multiple quality control (QC) measurements to assess the success of the library preparation and sequencing. If all the measurements indicate satisfactory results, we will not reprocess samples that have failed.
What is the turnaround time for whole plasmid sequencing?
We will sequence your plasmids typically within 1 business day.
For plasmids > 25 kb please except a turnaround time of up to 5 business days.
How about addressing the errors or positions with low confidence that I discovered in a homopolymer region or at a Dam or Dcm methylation site?
The prevalent error modes in Oxford Nanopore sequencing include deletions within homopolymer stretches, errors occurring at the central position of the Dcm methylation site CCTGG or CCAGG, and errors at the Dam methylation site GATC.
So please handle these regions with special care.