Amplicon Sequencing

Simple setup and fast results for amplicons of any size.

Amplicon PDP Header

Amplicon sequencing reimagined

Amplicon sequencing is central to applications such as targeted and viral genotyping, characterizing genome edits, construct verification, and library diversity analysis. Traditional approaches like Sanger or short-read NGS can slow progress with complex workflows, limited read lengths, and long turnaround times.

 

Plasmidsaurus delivers a faster, more scalable alternative. Sequence amplicons from 100 bp to 25 kb using the latest Oxford Nanopore Technologies platform. With no need for sequencing primers, library prep, or cleanup, generate high-quality data and go from experiment to insight in a matter of hours.
 

Hassle free insights

Hassle-free setup

Sequence any sized amplicon with easy ordering. No primers, library prep, or purification required.

No Primers copy

Accelerated science

Get your answers fast with linear/PCR results returned overnight and premium PCR results returned in 1-2 days.

De Novo

Streamlined insights

Automated reporting answers your most critical questions.

We’re moving faster!

We now deliver Premium PCR results overnight for samples in Seattle and San Diego!

Two services to meet your needs

Linear/PCR

Ideal for

Sequencing monoclonal PCR products

Typical applications

Determining or verifying the sequence of a DNA construct or genomic region
Whole viral genome sequencing

Sample input

Clonal, linear, double-stranded DNA

Service levels

Standard: 100 bp to 25 kb amplicons
Big: 25 - 125kb amplicons

Sequencing library

Amplification-free long-read library with minimal, random fragmentation

Data deliverables

One consensus sequence
Raw reads that map to the consensus

As fast as

Next day

As low as

$15

Premium PCR

Ideal for

Sequencing PCR products when working with mixed populations of molecules, or when sufficient read depth or full length reads are required

Typical applications

Characterizing CRISPR editing efficiency
Genotyping loci with heterozygous structural variants (insertions, deletions, etc.)
Quantifying and assessing library diversity
 

Sample input

Linear, double-stranded DNA

Service levels

Standard: Up to 3,000 reads / sample
Big: Up to 6,000 reads / sample
Huge: Up to 12,000 reads / sample
>12,000 reads / sample: Use Custom Sequencing
 

Sequencing library

Amplification-free long-read library with no fragmentation

Data deliverables

Up to 3 consensus sequences (if available)
Raw reads that map to your sample

As fast as

1 - 2 days

As low as

$30

Let us do the cleanup for you

PCR cleanup takes time better spent on real science. Add on cleanup for $5 and send us samples straight from the PCR machine—we’ll handle the rest. Get the same great results with less fuss.

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Key applications

Cloning

Confirm correct sequences at every step of your workflow.

Gene editing screening and confirmation

Characterize editing system performance and screen for cells with the right edit.

Genotyping

Verify or determine the genotype of your sample in the target region.

Viral genome sequencing

Accurate whole genome sequencing for viral evolution and epidemiological research, pathogen surveillance.

Characterize library diversity

Characterize the complexity and diversity of any linear-DNA based library.

Thumbs Up 2

"And thank you@plasmidsaurus for their quick PCR sequencing service that put me on the path to understanding. You guys provide a rock solid service. IMO you are to sequencing what NEB is to enzymes."

Yonathan Arfi
University of Bordeaux

Level up your amplicon sequencing

Plasmidsaurus
Sanger
Illumina (MiSeq)
Supports a wide range of amplicon sizes
From 100 bp to 125 kb. No more tiling!
With typical read lengths <1,000 bp, amplicon tiling is required for larger regions
Up to 600 bp (PE300), amplicon panels required for larger regions
Detects problems that can derail your research
Detects SNVs, indels and more complex rearrangements across any size amplicon
Misses low abundance mutations and limited by read length, PCR and sequencing primer design
Limited by short amplicon length and amplicon panel design
Minimal sample prep
No sequencing primers, library preparation, or sample cleanup required
Sequencing primers required
Library optimization and preparation required
Can characterize library diversity
Premium PCR has multiple read depth options to characterize complexity
Not possible
Can characterize library complexity
No minimum batch size
Results in 1-2 days no matter how many samples you send
Supports any number of samples
Time-delaying batching typically implemented to achieve cost efficiencies

Data deliverables & bioinformatics

Virtual gel

Frame 1171276157
The sequence of your amplicon in fasta, genbank (.gbk), and chromatograph (.ab1) file formats. For SNV confirmation and zygosity analysis, raw read support for each basecall is quantified in the chromatograph and per-base-data (.tsv) files.

Consensus sequence

Consensus sequence
The sequence of your amplicon in fasta, genbank (.gbk), and chromatograph (.ab1) file formats. For SNV confirmation and zygosity analysis, raw read support for each basecall is quantified in the chromatograph and per-base-data (.tsv) files.

Feature annotations

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Plasmidsaurus-provided annotations are automatically provided in the interactive feature map (online and downloadable) and the genbank file.

Reference alignment

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Automatic reference alignment identifies mismatches and associated protein consequences so you can immediately know whether your sample sequence is correct. Alignment results are reported online and in the downloadable comparison-results.tsv file.

Sequencing statistics including read length and coverage

Image 8
Histograms characterizing read length and coverage distribution across the consensus sequence as well as other sequencing metrics.

Raw reads

Frame 1171276161
Raw reads mapping to your consensus (linear/PCR) or sample (premium PCR) are provided in fastq format. Shows the distribution of read lengths in your sample — great for quickly identifying samples with unexpected PCR products.

For Premium PCR, please note that for complex mixtures where it is not possible to generate a consensus, only a virtual gel, read length histogram, and raw reads with annotations are returned.

Product specs & service levels

  • Long read sequencing with ONT
  • Optimized for clonal, linear, double-stranded DNA
Service LevelSizeMinimum VolumeConcentrationCostTarget Turnaround Time
Standard unpurified500 bp - 25 kb10 μL20 - 200 ng/μL$151 day
Standard unpurified + optional cleanup500 bp - 25 kb10 μL20 - 200 ng/μL$20
Standard purified500 bp - 25 kb10 μL20 - 200 ng/μL$15
Big purified25 - 125 kb20 μL20 - 200 ng/μL$30
  • Long read sequencing with ONT
  • Optimized for linear, double-stranded DNA
  • Add sample cleanup for $5
Service LevelCategoryTarget Read Depth/Sample*Minimum VolumeConcentration**CostTarget Turnaround Time
Standard100 bp - 25 kbUp to 3,000 reads10 μL1 ng/μL per 100 bp$302 days
Big100 bp - 25 kbUp to 6,000 reads10 μL1 ng/μL per 100 bp$60
Huge100 bp - 25 kbUp to 12,000 reads20 μL1 ng/μL per 100 bp$120

* Greater than 12,000 reads per sample can be accommodated through our Custom Sequencing Service.
** Premium PCR sequencing is based on the molarity of your DNA insert, therefore the required concentration (ng/uL) will vary depending on your insert size.

Ready to sequence?

Put your DNA in a tube and drop it off. Click below for requirements and suggestion for optimal results.

Step 1

FAQs

We sequence each sample with Oxford Nanopore long reads to very high depth before generating a consensus/assembly using the latest basecalling and polishing software:

  • We construct an amplification-free long-read sequencing library using the newest v14 library prep chemistry, including minimal fragmentation of the input linear DNA in a sequence-independent manner
  • We sequence the library with a primer-free protocol using the most accurate R10.4.1 flow cells (raw data is delivered in .fastq format).
  • We use the re-assembled raw reads to generate a high-accuracy linear consensus sequence from the raw reads.
  • For standard linear/PCR samples, we will also return a set of feature annotations.

As per Oxford Nanopore's specs for the chemistry and flowcells we currently use for Premium PCR sequencing, the consensus accuracy is typically >99.99%.

Results for the Linear/PCR service are typically returned next business day, and results for Premium PCR service are typically returned within 1-2 business days.

This is the average time it takes to return data to customers who are submitting orders from US, UK and EU. Turnaround times for customers in APAC may be slightly longer due to the time required in transit to our lab in Singapore.

Low sample quality can also negatively impact turnaround time and the quality of your results. Please read sample prep instructions carefully to make sure your samples meet input requirements. Due to variability in shipping logistics and sample quality that is outside our control we cannot guarantee turnaround times or sample success rates.

Our Linear/PCR product works in the same way as our Whole Plasmid service: you will receive an annotated assembled consensus of your submitted amplicon. The exact number of reads used to create this assembly varies based our internal quality control metrics, but is typically over a thousand.

The amount of sequencing coverage you will receive for Premium PCR is dependent on which option you choose:

CategoryAmplicon SizeRead DepthMinimum VolumeConcentrationCost (USD)
Standard100 bp - 25 kbUp to 3k reads10 μL1 ng/μL per 100 bp$30
Big100 bp - 25 kbUp to 6k reads20 μL1 ng/μL per 100 bp$60
Huge100 bp - 25 kbUp to 12k reads40 μL1 ng/μL per 100 bp$120

Linear/PCR samples are prepared using the same process as our Whole Plasmid service: the rapid barcoding approach from Oxford Nanopore Technologies. This makes use of a transposome complex to fragment the DNA, simultaneously preparing the ends for the attachment of the sequencing adapter. This is ideal for circular plasmids, as there will be one cut at some random point of the plasmid and the adapter will attach, resulting in full length plasmids. For a linear piece of dsDNA, it still needs to make a cut to attach the adapter and so none of the reads will be full length. For a clonal population of molecules, this doesn't pose a problem, and the fragments are straightforward to reassemble. As you might guess from the name, the rapid approach is lightning fast, and so our Linear/PCR service has the shortest possible turnaround time (one business day).

On the other hand, for a mixed population of molecules, reassembling is going to pose a problem because there is no way of knowing for certain which fragments originally belonged to which molecular species. So our Premium PCR samples are prepared using the native barcoding approach from Oxford Nanopore Technologies. This ligates the sequencing adapter to the ends of the molecules, preserving their full length which makes them extremely easy to tell apart—the single molecule nature of the sequencing platform means that each read corresponds to one specific molecule. This library prep is less rapid, which is why there is a slightly longer turnaround time (one to two business days).