Sample type | Category | Size | Concentration | Minimum volume | Price per sample | Order now |
---|---|---|---|---|---|---|
Plasmid | Standard | 2.5 - 25 kb | 30 ng/uL | ≥10 uL | $15 or 1 dinocoin | Order |
Big | 25 - 125 kb | 50 ng/uL | ≥20 uL | $30 or 2 dinocoins | Order | |
Huge | 125 - 300 kb | 50 ng/uL | ≥40 uL | $60 or 4 dinocoins | Order | |
Linear/Amplicon | Standard | 600 bp - 25 kb | 30 ng/uL | ≥10 uL | $15 or 1 dinocoin | Order |
Big | 25 - 125 kb | 50 ng/uL | ≥20 uL | $30 or 2 dinocoins | Order | |
Bacterial Genome | Standard | up to 7 Mb | 50 ng/uL | ≥20 uL | $90 or 6 dinocoins | Order |
Big | 7 - 12 Mb | 50 ng/uL | ≥20 uL | $105 or 7 dinocoins | Order | |
Standard with extraction | up to 7 Mb | Send a bacterial pellet in DNA/RNA Shield | $105 or 7 dinocoins | Order | ||
Big with extraction | 7 - 12 Mb | Send a bacterial pellet in DNA/RNA Shield | $120 or 8 dinocoins | Order | ||
Hybrid ONT + Illumina | up to 7 Mb | 50 ng/uL | ≥20 uL | $165 or 11 dinocoins | Order | |
Big Hybrid ONT + Illumina | 7 - 12 Mb | 50 ng/uL | ≥20 uL | $195 or 13 dinocoins | Order | |
Hybrid with extraction | up to 7 Mb | Send a bacterial pellet in DNA/RNA Shield | $180 or 12 dinocoins | Order | ||
Big hybrid with extraction | 7 - 12 Mb | Send a bacterial pellet in DNA/RNA Shield | $210 or 14 dinocoins | Order | ||
Pre-paid credits | Dinocoins | $15 | Purchase |
In all cases, samples are sequenced without primers or amplification. Please do not ship any primers with your samples or mix primers into your samples. 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 strongly recommend using Qubit or equivalent to measure DNA concentration. Nanodrop is NOT ADEQUATE due to low accuracy.
No. Nanodrop is NOT ADEQUATE for DNA quantification due to low accuracy. The extent to which Nanodrop is off varies widely depending on the specific composition of your sample, so there is no standard way to “adjust” Nanodrop values. Sending samples at too high OR too low concentration based on Nanodrop values may adversely affect the library prep and/or sequencing reactions, possibly resulting in sequencing failure.
Please register for an account. When you log in, you will be directed to your Dashboard and will see options on the screen to submit your order.
You can cancel an order from the order details page, reached via the magnifying glass button on your Dashboard.
We will accept any number of sample(s).
Yes, absolutely!
Our Dropboxes and the free & reduced cost UPS labels generated during order submission both provide overnight shipping within the US to our Louisville lab location, and both provide next-morning results for whole plasmid and linear/amplicon sequencing. We recommend that US customers use either a Dropbox or a plasmidsaurus-generated UPS label whenever possible (rather than self-shipping).
International Dropbox shipments are usually delivered to us within 2-3 days and we provide results on the same morning of receipt. If you do not have a local dropbox, you can self-ship via any carrier to our Louisville lab location:
plasmidsaurus
4743 Poplar Level Road
Louisville, KY 40213
Please ensure any required forms are included with your shipment.
NOTE ABOUT DROPBOXES: The specific day that each dropbox ships out varies by site, and may not be every weekday for your local dropbox. Please check the dropbox list to find the shipping day(s) for your local dropbox! To ship your samples on a different day, please refer to "Alternative Shipping Options" in the detailed shipping table. Contact us at plasmids@snpsaurus.com if you’re interested in hosting a new dropbox at your location!
The free & reduced cost UPS labels generated during order submission provide overnight shipping within the US to our Eugene lab location and provide results within 1 business day for bacterial genome sequencing. We recommend that US customers use the plasmidsaurus-generated UPS label whenever possible (rather than using a Dropbox or self-shipping).
Free & reduced cost UPS labels are only available to US customers at this time, therefore for international customers, using a Dropbox will provide fastest turnaround time. International Dropbox shipments are usually delivered to us within 2-3 days and we provide results within 1 business day of receipt. If you do not have a local dropbox, self-ship via any carrier to our Eugene lab location:
plasmidsaurus
1850 Millrace Drive, Suite 200
Eugene, OR 97403
Please ensure any required forms are included with your shipment.
NOTE ABOUT DROPBOXES: The specific day that each dropbox ships out varies by site, and may not be every weekday for your local dropbox. Please check the dropbox list to find the shipping day(s) for your local dropbox! To ship your samples on a different day, please refer to "Alternative Shipping Options" in the detailed shipping table. Contact us at plasmids@snpsaurus.com if you’re interested in hosting a new dropbox at your location!
If you placed an order of 8+ plasmids/amplicons, 4+ Bigs, 2+ Huges/Bacteria or larger and requested a free domestic UPS shipping label it will be automatically downloaded at the order confirmation screen to your browser’s download folder.
We update your Dashboard with the received date immediately upon opening your package. If you do not see a received date in your Dashboard, then we have not yet received your samples, although we may be still in the process of opening packages that have been delivered. Keep an eye on your Dashboard for updates.
No, your package will be held by the carrier and delivered to us on Monday. Plasmids and high-quality bacterial genomic DNA are quite stable, so the wait isn't a problem.
Please Check our Dropbox Map or the Dropbox List to find a plasmidsaurus dropbox near you. You can find information about dropbox pick-up times and locations on the map or from the list.
If there isn't one at your institution yet, we are interested in setting one up! Contact us at plasmids@snpsaurus.com if you are willing to host one.
First go to the Dropbox List on our website and search for the dropbox that was used for shipping us your samples. Once there, click the “UPS” button to the left of the dropbox entry under the “Tracking” column. This will take you to a new page with a list of tracking numbers and the date the corresponding shipment should be sent out. Just click the tracking number for the shipment from the week your samples were submitted and it will take you to the UPS tracking page for that shipment.
You don’t need to notify us in order to have your samples collected from our dropboxes. Any and all orders that are dropped-off in one of our dropboxes will be packaged and shipped to us on the listed cut-off day/time posted on the dropbox and on our website.
Look us up under the company name SNPsaurus
Never any extra fees! The prices listed in the table above are what we will charge you.
Please generate your own quote using our quote tool!
You can pay by credit card, purchase order (PO), or dinocoins at the time of submission. You can also elect to have a credit card payment link emailed to a purchasing agent at your institution. If you need to make alternate payment arrangements, email us at remit@snpsaurus.com.
If you will be placing multiple orders using purchase orders,
please consider using a blanket PO (also called a standing PO) or dinocoins.
This simplifies the ordering process for you and the invoicing process for us.
Blanket POs can be used by individuals or a lab group.
Get a quote for the amount
you think you will use over the next few months and your purchasing department will issue a PO for
that amount.
Check first - not all organizations allow blanket POs.
You would use that PO number every time you order and we invoice the blanket PO every month or so.
Tired of dealing with credit cards and purchase orders? Got a grant that's expiring? Load up on dinocoins!
Dinocoins are pre-paid credits that can be used to pay for sequencing. When you have Dinocoins in your account, you can “apply Dinocoins” during checkout to pay for an order.
Dinocoins never expire and hold their dollar value. No need to worry about future price drops when buying dinocoins.
Dinocoins cannot currently be used to partially pay for orders -- it's all or none.
You can pay for Dinocoins by credit card, payment link or PO.
If you order using a payment link, the Dinocoins will not be available in your account until the link is paid.
If you use a PO, you must purchase Dinocoins from your Dashboard on
the
plasmidsaurus website (see the last row of
the order table) to populate your account with the Dinocoins. You can see all your transactions and the number of
Dinocoins you have left on your Dashboard so it is easy to monitor
usage.
For credit card orders, invoices are issued at the time of placing an order to the email address
associated with the submission account.
Credit card invoices can also be downloaded from your Dashboard.
For POs, invoices are generally issued on a monthly basis to the billing address listed on the
PO.
In the vast majority of cases, we deliver plasmid sequencing results:
Please see How to ship whole plasmid and linear/amplicon sequencing samples to get the fastest turnaround time?
Our service for plasmids is intended for a clonal population of molecules. You can send mixtures of molecular species, but since we can't predict the analysis outcome, it's at your own risk.
Sequencing is considered successful if the pipeline is able to generate any consensus, even if it is not your target. Re-sequencing mixtures won't change the relative proportions of the species, but you can submit multiple aliquots if you need higher total coverage.
If the pipeline does not produce a consensus for your target, you can download the raw reads from your Dashboard and bin them yourself.
If you are interested in sequencing a known mixture (e.g. barcode or variant libraries), please refer to the section below on Custom Sequencing Service.
As per Oxford
Nanopore’s specs for the chemistry
and flowcells we currently use for plasmid sequencing, the raw read accuracy is
>99%.
Deeper coverage — meaning more reads from which to build a consensus —
generally increases the accuracy of results.
The most common error modes for Oxford Nanopore are deletions in homopolymer stretches and errors at the Dam methylation
site GATC.
This limitation is expected to improve with future updates
to
their sequencing chemistry and basecalling software.
We do not guarantee any specific level of coverage.
The number of raw reads generated can vary substantially
depending
on sample quality.
Successful samples sent at the required concentration typically yield in the high dozens to
hundreds
(or thousands!)
of raw sequencing reads.
Final coverage of the consensus depends on how many of the raw sequencing reads are full-length
plasmids
and
whether any degraded plasmid reads can be aligned to the full-length consensus.
Average coverage is reported in the header line of the fasta file. Coverage over ~20x
indicates a very accurate consensus.
Finally, we return two files that show how confident we are in our basecall at each position of our consensus sequence:
Note we do not return chromatograms (.ab1 files) because we do not do Sanger sequencing. The confidence files described above provide similar information.
The histogram displays raw read lengths between 1-25kb (for standard plasmids) and is subdivided into 100 bins. Before sequencing your plasmids, we linearize them so that we get mostly full-length sequence reads. As a result, the lengths of our raw sequencing reads reflect the lengths of the molecular species in your sample.
Ideally, your target plasmid will be the only species in the sample, and we will see one dominant peak in the read length histogram:
(Please note that even a single apparent peak MAY contain multiple plasmids of the same size, or multiple plasmids of different lengths that happen fall into the same histogram bin. Sequences that are very similar are assumed by the analysis pipeline to be variations of a single species and it will attempt to make a single consensus (with potentially low confidence positions reported in the stats.txt file); if the sequences are very distinct, it will attempt to produce multiple consensus sequences.)
If your raw reads contain varying numbers of indels (common for noisy raw reads), this may sometimes cause the read lengths to straddle a bin boundary and artifactually create an appearance of two separate peaks:
(Please note that a peak straddling a bin boundary MAY contain multiple plasmids of the same size, or multiple plasmids of different lengths that happen fall into two adjacent histogram bins. Sequences that are very similar are assumed by the analysis pipeline to be variations of a single species and it will attempt to make a single consensus (with potentially low confidence positions reported in the stats.txt file); if the sequences are very distinct, it will attempt to produce multiple consensus sequences.)
More often than you would expect, though, we see multiple peaks corresponding to multiple plasmids, or a peak of a different size than the customer expected:
(The analysis pipeline will provide consensus sequences for any plasmids in the mixture that obtain enough coverage and are at least 20% the height of the max peak in the sample. If you observe a histogram peak here that does not have an accompanying consensus delivered in your data, then coverage of that species was too low to assemble or that peak was actually a mixture of plasmid species. If sequencing fails entirely due to low coverage for all species in the mixture, you will not receive any consensus sequences, but you may find some useful information in the raw reads.)
Occasionally we see a sample with a dominant peak in addition to an abundance of degraded DNA (genomic and/or plasmid). In some cases the dominant peak may still produce a consensus, if read coverage and accuracy are sufficient:
Sometimes we see a decent number of reads for the sample but there is NO dominant peak, indicating an abundance of degraded DNA (genomic and/or plasmid) from a poor plasmid prep, or that the strain contains no plasmids:
Often, the read count is too low to distinguish any peaks or to generate any consensus:
For plasmids, “failure” refers to the failure of your sample to produce a consensus sequence with at least 10x coverage.
Our low sequencing prices and fast turnaround times do not include extensive QC to determine why plasmid samples fail. Although we do not provide definitive reasons for failure, by far the most common reasons are:
To achieve optimal sequencing results, please follow our recommended sample prep and QC steps.
It is relatively rare that we cannot return a plasmid sequence, but some rate of failure is unavoidable. We may attempt to re-sequence failed samples if your sample quality and quantity permits (with follow-up results delivered in 2-3 business days). If the sample fails a second time, we will conclude that something about the sample makes it unsequenceable. Check out our Sequencing Workflow. Unfortunately we must still charge for failed samples, since we spend more time and resources on them than we do on successes.
In the vast majority of cases, we deliver linear/amplicon sequencing results:
Please see How to ship whole plasmid and linear/amplicon sequencing samples to get the fastest turnaround time?
Our service for linear/amplicons is intended for a clonal population of molecules. You can send mixtures of molecular species, but since we can't predict the analysis outcome, it's at your own risk.
Sequencing is considered successful if the pipeline is able to generate any consensus, even if it is not your target. Re-sequencing mixtures won't change the relative proportions of the species, but you can submit multiple aliquots if you need higher total coverage.
If the pipeline does not produce a consensus for your target, you can download the raw reads from your Dashboard and bin them yourself.
If you are interested in sequencing a known mixture (e.g. barcode or variant libraries), please refer to the section below on our Custom Sequencing Service.
As per Oxford
Nanopore’s specs for the chemistry
and flowcells we currently use for linear/amplicon sequencing, the raw read accuracy is
>99%.
Deeper coverage — meaning more reads from which to build a consensus —
generally increases the accuracy of results.
Depending on the sequence of your sample, the assembler does sometimes have difficulty reconstructing the terminal ends of linear DNA, which may result in up to ~25 nucleotides missing from the 3’ and/or 5’ ends of your insert. If you observe this happening with your samples, you may download the raw reads from your Dashboard and reconstruct the ends with your preferred method.
The most common error modes for Oxford Nanopore are deletions in homopolymer stretches and errors at
the
middle position of the Dcm methylation
site CCTGG or CCAGG.
This limitation is expected to improve with future updates
to
their sequencing chemistry and basecalling software.
We do not guarantee any specific level of coverage.
Number of raw reads generated can vary substantially
depending
on sample quality.
Successful samples sent at the required concentration typically yield in the high dozens to
hundreds
(or thousands!)
of raw sequencing reads.
Average coverage is reported in the header line of the fasta file. Coverage over ~20x
indicates a very accurate consensus.
Finally, we return two files that show how confident we are in our basecall at each position of our consensus sequence:
We do not return chromatograms (.ab1 files) because we do not do Sanger sequencing. The confidence files described above provide similar information.
We do not return histograms for linear samples because these samples are fragmented during library prep, thus a clonal peak is not produced on the histogram and it is typically not informative.
For linear/amplicon, “failure” refers to the failure of your sample to produce a consensus sequence with at least 10x coverage.
Our low sequencing prices and fast turnaround times do not include extensive QC to determine why samples fail. Although we cannot provide definitive reasons for failure, by far the most common reasons are:
To achieve optimal sequencing results, please follow our recommended sample prep and QC steps.
It is relatively rare that we cannot return a linear/amplicon sequence, but some rate of failure is unavoidable. We may attempt to re-sequence failed samples if your sample quality and quantity permits (with follow-up results delivered in 2-3 business days). If the sample fails a second time, we will conclude that something about the sample makes it unsequenceable. Check out our Sequencing Workflow. Unfortunately we must still charge for failed samples, since we spend more time and resources on them than we do on successes.
In the vast majority of cases, we deliver bacterial genome sequencing results within 1-2 business days of receipt of your samples. When our genomic DNA extraction option is selected, we deliver bacterial genome sequencing results within 1 week of receipt of your samples. If you select the NEW Hybrid sequencing option, we deliver hybrid results with 6-8 business days (or 8-10 business days if you include the extraction option).
As per Oxford
Nanopore’s specs for the chemistry
and flowcells we currently use for bacterial genome sequencing, the raw read accuracy is
>99%.
The accuracy of the final assembly varies depending on coverage and data
quality.
Deeper coverage — meaning more reads from which to build a consensus —
generally increases the accuracy of results.
Successful sequencing is defined by achieving at least one of the following deliverables:
However, our ability to deliver these target outputs is directly dependent on the quantity, quality, and purity of the gDNA that is sent to us. We do not guarantee any specific output.
1. Remove the bottom 5% worst fastq reads via Filtlong v0.2.1 (default parameters)
2. Downsample the reads to 250 Mb via Filtlong to create a rough sketch of the assembly with Miniasm v0.3
3. Using information acquired from the Miniasm assembly, re-downsample the reads to ~100x coverage (do nothing
if there isn't at least 100x coverage) with heavy weight applied to removing low quality reads (helps small plasmids
stick around)
4. Run a Flye v2.9.1 assembly with parameters selected for high quality ONT reads
5. Polish Flye assembly via Medaka v1.8.0 using the reads generated in step 3
6. Run several analyses:
If you select the NEW Hybrid sequencing option, we target the same deliverables listed above for your ONT-only assembly, PLUS we run the following additional step:
7. Polish the ONT .fna assembly with Illumina .fastq reads using Polypolish v0.5.0, which yields a new .fasta polished hybrid assembly file
If you select the NEW Hybrid sequencing option, we deliver the same files listed above for your ONT-only assembly, PLUS we deliver the following additional file:
If we are not able to achieve at least one of the target deliverables, then we will repeat sequencing as per our bacterial repeat policy.
Even when a high-quality assembly cannot be generated, we still provide the raw data and the report, and you may also still receive some of the other file types.
Although we do not provide definitive reasons on why each specific sample may need to be repeated, by far the most common reasons are:
To increase chances of successful sequencing on the first attempt, please adhere closely to our sample prep guidelines.
If we are not able to achieve at least one of the target deliverables on the 1st sequencing attempt, we will evaluate the results of the initial sequencing attempt to determine whether additional sequencing may produce a more successful outcome, and if so we will repeat the sequencing (with possible protocol adjustments) at no additional charge. We will also combine the data from the two runs together to increase chances of success on the repeat.
If we are not able to achieve at least one of the target deliverables on the 2nd attempt, we will not perform further repeats.
If you wish to sequence the sample again, please prepare new samples that meet all the QC requirements before submitting a new sequencing request.
This service is intended for a clonal population (single species) of bacteria. You can send mixtures of different bacterial species for sequencing, but since we can't predict the assembly outcome, it's at your own risk.
The total amount of raw data obtained for your sample will be divided up between however many species are present in your sample, thereby reducing each species’ own genome coverage and possibly inhibiting assembly of particular species in the sample. Re-sequencing mixtures won't change the relative proportions of the species, but you can submit multiple aliquots if you need higher total coverage. Ultimately, which species end up producing an assembly will vary depending on overall sample quality, coverage, and relative abundance/degradation of each species.
If your gDNA extract also contains native plasmid DNA, then yes, you will probably receive some sequencing reads for those plasmids. Input DNA fragments < 3kb are typically omitted during the sequencing process, but otherwise we do not filter out small plasmid-sized reads during assembly, so it is likely that they will also produce their own plasmid assemblies in addition to the gDNA assembly. Ultimately, which types of DNA in your sample end up producing an assembly will vary depending on overall sample quality, coverage, and relative abundance/degradation of each type of DNA.
Yes, any species can technically be sequenced and assembled with this method, but submitting samples for non-bacterial applications is at your own risk since we have not optimized the amount of data required for each specimen type and our assembly/annotation pipeline is targeted for bacteria. You may need to submit multiple aliquots of each sample in order to get enough genome coverage for these larger, more complex eukaryotic genomes (and note that you would need to combine data from all your aliquots prior to running your own assembly pipeline). If you are planning to submit a large number of samples for such an off-label application, contact us prior to submission to discuss options.
If you are interested in sequencing a known mixture (e.g. barcode or variant libraries), please send us an email at plasmids@snpsaurus.com to set up a custom project so that we can collect the amount of data you require.
Since our standard pipeline won't be able to generate a consensus from your mixture, we will send you the raw reads for you to analyze yourself; however we are able to use the newest ONT chemistry for these custom preps, which now delivers >99% accurate raw reads!
Probably! Email us at plasmids@snpsaurus.com to discuss your project details.
In the vast majority of cases, we deliver custom sequencing results within 3-5 business days of receipt of your samples.
As per Oxford Nanopore’s specs for the chemistry and flowcells we currently use for custom project sequencing, the raw read accuracy is >99%. We do not provide a consensus or assembly for custom projects; we provide the raw reads and you need perform your own analyses, which will dictate your final data accuracy.
Custom projects require us tailoring our sequencing service to meet each customer's experimental needs. Please email us at plasmids@snpsaurus.com to discuss and initiate your project.
The cost for each custom sequencing project is calculated as follows:
Total Data Required = Number of samples x Insert length x Number of species/barcodes/variants x
Coverage required per variant
Project Cost = $500 base price for 1st Gb data + $50 for each extra Gb data + $50 for barcoding each
sample
Custom projects start at $500 for up to 1 Gb of total raw data and add $50 for each additional 1 Gb. There will also be a $50 per-sample barcoding surcharge added for projects with more than 1 sample. We will provide you a price estimate (and custom quote if you need it) when you email us to discuss your project.
We provide only the raw reads (>99% accurate) for custom projects. You would need to perform analyses (demultiplexing barcodes, generating consensus, aligning variants, etc.) yourself.
I submitted plasmids and got amazing results! This changes the way I do my research!
Let your friends and social media followers know about us
-- the more volume we get, the more we can lower our prices and turnaround time.
Have a suggestion for how to improve our service?
Let us know at plasmids@snpsaurus.com.
Just got my plasmid sequencing results back from @plasmidsaurus and the insert is perfecto. Even fixed some legacy mis-sequencing from looong ago. Only 3 SNPs after 10 years of use. I *highly* recommend their services and for everyone to sequence their *entire* construct. pic.twitter.com/7QOaANo5fa
— Sebastian S. Cocioba (@ATinyGreenCell) October 1, 2021
Don’t sleep on @plasmidsaurus for your whole plasmid sequencing. Price right. Data right. Turnaround time tight. And the auto annotation feature is a nice bonus. Plus these guys outta Eugene #oregonstrong #oregonlong…readsequencing https://t.co/vthGoROL0t
— Arpiar Saunders PhD (@your_arpy) October 1, 2021
Tired of Sanger sequence just a fraction of your plasmid? Having them failing because of not having a good annealing region? These guys are awesome and we use their ehoke-plasmid sequencing all the time. https://t.co/WAIgsvAX39
— Alex Bisson (@Archaeon_Alex) September 15, 2021
If you're looking for whole plasmid sequencing, definitely check out @SNPsaurus. Sent out samples Thursday evening and had (great) results back by midnight Friday. Very affordable and would highly recommend.
— Josh Currie (@_Josh_Currie) July 5, 2021
A surprising fraction of the plasmids we sequence have an unexpected assembly size. Here is a good example: https://t.co/Y9PyNMufuA
— SNPsaurus (@SNPsaurus) August 17, 2021