The right answers to frequently asked questions
Find the answers to all our products and services by clicking the links below.
When should I use the Custom Long-Read Amplicon Sequencing service instead of the ONT Lite Clonal Amplicon Sequencing service?
Custom Long-Read Amplicon Sequencing dedicates an entire flow cell to your amplicons. As a result, this method is more time-consuming and costly compared to ONT Lite Clonal Amplicon Sequencing service, but it is highly suitable in the following cases:
- When you need additional services like 16S Microbiome Analysis, Unique Sequence Analysis, Variant Analysis, Sequence Cleaning, Host Removal, Pod5 raw data delivery
- When your linear DNA sample is not clonal but instead contains a mix of different molecules.
- When full-length, end-to-end reads are required, without any fragmentation.
- When full-length assemblies without missing terminal nucleotides are required.
- When a higher number of sequencing reads is needed beyond the typical output of the ONT Lite Clonal Amplicon Sequencing service.
- When you need to obtain all raw reads generated from your sample.
How should I purify my amplicons?
We recommend purifying your amplicons with commercially available kits based on DNA-binding beads or columns or enzymatic cleanup. DO NOT ship any primers with your samples or mixed into your samples.
What types of samples can be submitted for amplicon sequencing?
Submit purified PCR products with a size range of 500 bp to 25 kb. The amplicons should ideally produce a single band on a gel for optimal results.
Does Eurofins Genomics perform a QC on my samples before library preparation?
Yes, we do perform a QC of the quantity of the amplicons.
I have mixed amplicons in a single sample that I want to sequence. Can I get the unique sequences from this mixture, and how can your service help with this?
Yes, you can send in a single sample containing mixed amplicons for sequencing. Our Unique Sequence Analysis service is specifically designed to handle such samples. By using advanced sequencing and bioinformatics techniques, we can accurately separate and identify each unique sequence, ensuring you get comprehensive and reliable results from your mixed amplicon sample.
How can I order my needed service?
Please go to our website https://eurofinsgenomics.eu/, select your wished service and follow the instructions. Depending on the selected product you might need to raise a quote first. Once your quote is available you will be informed, and you can accept it in your account (please navigate to “Account” -> “Quotes”).
During the ordering process you will be asked to upload your samples via our Sample Submission Sheet. You can find the option to download the sheet directly next to the upload button (please always download the sheet here as it can differ between the products we offer). This sheet requires you to give us more information about your samples, as well as assigning Eurofins NGS Barcode Labels to your samples.
How can I get Eurofins NGS Barcode Labels?
Our Eurofins NGS Barcode Labels can be ordered (free of charge) on our website (“Quick Order” -> “Next Generation Sequencing” -> “Additional Services” -> “NGS Barcodes & UPS labels”) and after a few days you will receive your labels. Please stick them on your tubes based on the assignment you made on the Sample Submission Sheet. Please note that we can only accept samples arriving on our laboratory that are labelled with our Eurofins NGS Barcode Labels.
You can also find a list of your Eurofins NGS Barcode Labels at “Account” -> “NGS Barcodes & Coupons” -> “NGS Barcodes”.
How can I monitor the progress of my order?
Your order can be tracked in your Eurofins account. Please navigate to your “Account” -> “Orders” -> “My Orders”. Here you can see all your orders listed. For more detailed information please klick on the Tracking Details icon. It leads you to our Order Tracking page where you can find all your samples and their current status.
How can I send my samples to Eurofins?
Please note that Eurofins Genomics has different sites in Germany. Therefore, please make sure you are shipping to the correct site as instructed by your quote or sales representative.
If you require UPS labels you can order them on our website (https://eurofinsgenomics.eu/en/next-generation-sequencing/ngs-barcodes/ - “Quick Order” -> “Next Generation Sequencing” -> “Additional Services” -> “NGS Barcodes & UPS labels”) and after a few days you will receive your UPS labels.
How accurate are the sequencing results?
According to Oxford Nanopore's specifications for the chemistry and flow cells we currently use, the consensus accuracy is typically greater than 99.99%
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.
How can I access my data?
Login to your Eurofins account with your e-mail address and password at https://www.eurofinsgenomics.eu/ and click on “My Orders”, then on your OrderID. You will find the files under section “DOWNLOAD DOCUMENTS & FILES”.
If you have received any compressed files, we recommend 7-ZIP (https://www.7-zip.org/) to uncompress them. Files will be deleted from our server 8 weeks after delivery.
Alternatively, you can access your data via our FTP server at ngs-ftp.eurofinsgenomics.eu using the username (the "ftp-" is part of the username) and password that you will receive in an email once your first data gets delivered. If you have forgotten your password, please enter ngs-ftp.eurofinsgenomics.eu to your browser and choose the "Forgot your password?" option.
Should you encounter any issues or have any queries, please do not hesitate to contact us.
Will my data be secure at Eurofins?
We prioritize data security and make every effort to keep your data private and protected. Our data transfer methods are secure; however, if you prefer an alternative delivery method, we are happy to accommodate your request.
What type of analysis is provided for Custom Long Read Amplicons?
Various analyses can be selected during ordering, including 16S microbiome, consensus sequence analysis, variant detection and unique sequence identification, are available depending on your project's specifics. If you require a special analysis, please reach out to your sales representative.
What data & file types will I receive?
- Raw Nanopore amplicon data (FASTQ)
- Raw Nanopore sequencing data (POD5) available on request (additional costs)
- Customizable data analysis packages are available in our ordering form
- Variant analysis
- Variant (SNPs & InDels) Calls (TSV)
- Analysis Report (HTML)
- 16S Microbiome Analysis
- OTU Quantification Tables (TSV)
- Analysis Report (HTML)
- Unique Sequence Analysis
- Unique Sequences (FASTA)
- Clustering quantification table (TSV)
- Analysis Report (HTML)
- Consensus Sequence Analysis
- Consensus Sequence (FASTA)
- Variant Calls (TSV)
- Analysis Report (HTML)
What if my results do not match my expectations?
If you believe a processing error may have occurred, please contact us, and we will investigate on a case-by-case basis.