Plasmid sequencing

e-Zyvec supports you in your high throughput plasmid sequencing projects.

Overview

Plasmid sequencing workflow

workflow plasmid sequencing

e-Zyvec’s Plasmid Sequencing service use the power of Next Generation Sequencing for plasmid verification (obtaining the complete sequence of any plasmid). Unexpected mutations and erroneous sequence information can affect downstream applications and lead to unnecessary troubleshooting slowing down the progress of your research.

Our platform offers a streamlined workflow, and more data from less sequencing. This has enabled the e-Zyvec team to develop a high-quality, high-throughput service for complete plasmid sequencing and de novo assembly.

Our Turnaround time is 2-3 weeks from sample reception or 3 working days in express!

Plasmid sequencing analysis

We have developped our inhouse analytic pipeline. Based on NGS raw data obtained using Illumina technology, we combine read mapping and de novo assembly to generate a report for each molecule analysed.

Each one of these reports was individually evaluated to ensure consistency between the expected and delivered products.

Aside from the first report, we provide the following files in the provided result folder:

. If the next generation sequencing results is consistent enough with the theoric sequence of a vector, we provide you the corrected sequence wich corresponds to your theoric sequence but integrating the variations found in the NGS analysis.

. If the next generation sequencing results are not consistent with the theoric sequence (for example large insertions or deletions), we provide you a de novo assembly. Note that there may be several sequences (contigs) in this fille in case of fragmented assembly.

plasmid sequencing results

Concentric plot summarizing the plasmid sequencing with coverage plot of the NGS read mapping

Service detail / Pricing

Plasmid sequencing Price

For each project, you will have the possibility to pay on the basis of completes series (12, 24, 48, 72, or 96 samples), or per samples. 

For example, if you have 22 samples to sequence, you will pay for a run of 13 to 24 samples, or for 22 samples multiply by the price affiliated with your status. 

A complete series will be automatically in express (3 workings days).

Prices for a complete series:

up to 12

(from 155€/rxn)
1850 /run
  •  

13 to 24

(from 88€/rxn)
2105 /run
  •  

25 to 48

(from 54€/rxn)
2570 /run
  •  

49 to 72

(from 41€/rxn)
2960 /run
  •  

73 to 96

(from 31€/rxn)
3160 /run
  •  
Prices for individual sample:

1 sample

160 /rxn
  •  

One reaction (rxn) will generate approximately 15Mb of data ensuring a deep coverage of the plasmid.

Prices include automated bioinformatic analysis (de novo assembly and optional comparison to available in silico reference).

How to order

STEP 1:

LOG INTO OUR ONLINE PLATFORM

STEP 2:

CREATE YOUR OWN PROJECT

STEP 3:

SUBMIT YOUR PROJECT

Faq

Samples must be sent to e-Zyvec SAS, NGS, 80 rue du Dr Yersin, 59120 Loos – FRANCE.

To ensure a good process, please send between 10-25µL volume of your template (≥50ng/µL) witch means at least 500ng.

If your samples are less than the amounts indicated let us know we can provided further assistance. Samples must be in a Nuclease-free H2O or 10 mM Tris-HCl pH 8.0 solution. The reference purity is to have an OD A260/A280 ratio ≥ 1.8 and A260/230 ≥ 1.9.

We have developped our inhouse analytic pipeline. Based on NGS raw data obtained using Illumina technology, we combine

read mapping and de novo assembly to generate a report for each molecule analysed.

We operate routine sequencing of purified plasmids whatever their size (so far, we went up to 23Kb). However, using our ISeq100, we can also analyze other DNA molecules such as PCR amplicons, Cosmids or Bacmids, RNAs (RNAseq), or genomic DNA. Such projects will be undertaken as ‘tailored-projects’, so please, contact us for feasibility assessment and quotes.

A PDF report will be sent by e-mail (you can also download the results in your project management page on www.e-zyvec.fr) to you summarizing the analysis of your sequences, in addition to this report, we provide various files:

. If the results are consistent enough with the expected sequence of a given vector, we provide you the corrected sequence (_corrected.fasta) highlighting the differences found.

. If the results are not consistent enough with the expected sequence (for example large insertions or deletions), or if an expected sequence was not communicated, we provide you a de novo assembly file (_assembly.fasta). Note that there may be several sequences (contigs) in this file in case of fragmented assembly, and that you may have to further analyze these results.

Incomplete assembly may occur for various reasons:

1- In case there are long (>300bP) repeated sequences in your molecule (promoter duplication for example) NGS analysis will not be able to confirm that all duplications are effectively present. In such case we may operate complementary analysis upon to confirm duplications, upon demand, or advise you on how to proceed for such validation by yourself.

2- Extreme High or Low GC content may result in sub-optimal reading with Illumina technology (as well as for any known technology). If such difficult sequences stretch over long (>300bp) portions of your molecule this may impair the analysis locally.

3- Mixed samples (contamination of your vector with another vector or too much genomic DNA) will result in several contigs that cannot be discriminated.

On top of the technical quality control recommended by Illumina and reagents manufacturer, we have included some analysis controls in our pipeline. One of these is the ratio of reads unmapped to the expected sequence.

If too high it would indicate a sample contamination by either another plasmid or some genomic DNA, or even the presence of unexpected material inserted within your vector.In such case we will provide you the corresponding contigs assembled from the unmapped data (if any relevant).

The regular service is based on a unit price for each reaction, and the estimated time is 2 to 3 weeks. Basically, your samples are queuing until the next available run (so it might be quicker than the estimated times if you’re lucky).

The express service time is estimated at 3 days, this service being available for orders up to 12, 24, 48, 72 and 96 reactions. In this case we are dedicating a full run to your analysis, hence the short delay.

These services do not differ on the sequencing methodology employed, or the analytic pipeline for plasmids validation.

Contact-us

Let's Talk

Laboratory

e-Zyvec – 80 rue du Docteur Yersin
59120 Loos
FRANCE
+33 (0)3 59 61 50 43

Headquarters

Vectura – HQ
75 Rue Marguerite Perey
67400 Illkirch
FRANCE
+33 (0)3 90 40 61 80

Stay tuned