Short-Read Whole Genome Sequencing (WGS)

Precision Short‑Read Whole Genome Sequencing

Key Benefits of Our Whole Genome Sequencing Services

WGS Bacteria, Fungi, Yeast

WGS Human, Mammals, Plants

De novo assembly or comprehensive SNP/variant analysis?

Need something else?

NGS Prepaid Coupons

NGS Sample Submission

Free Barcodes, UPS Labels, Dropbox usage

Quality is important for us at Eurofins

Quick Start

Reliability

Accuracy

Flexibility

Expertise

Secure data

Product specifications

Additional services & important links

Frequently Asked Questions

Related Items

Our products and services are produced and performed under strict quality management and quality assurance systems.

Reliable Genomic Insights From High‑Throughput Sequencing

Highlights for short-read WGS

Applications for short-read WGS

Comprehensive Genome Sequencing Workflow

Library Preparation

Sequencing

Sequencing depth

Coverage recommendation

Coverage calculation

DISCOVER our flexible DNA ANALYSIS solutions

De novo assembly

Variant detection

Custom bioinformatics analysis

Whole Genome Sequencing (WGS) with Illumina short-read technology offers high-precision sequencing with exceptional accuracy, enabling the detection of single nucleotide variants (SNVs) and small InDels.

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Flexible solutions for non-human and non-prokaryotic samples, including animals, plants, yeast, other eukaryotes, or viruses.
Short turnaround times starting from 12 working days
Unique Dual Indexing (UDI) ensures high-quality data.
Scalable data output, starting from 5M read packages
Highly sophisticated bioinformatics services & interactive analysis reports
Optional DNA isolation service
Data transfer via secure FTP

Resequencing of whole genomes
Our standard Variant Analysis service includes detection and annotation of germline single nucleotide polymorphism (SNPs), insertions and deletions (InDel).
Additionally, we provide optional services such as structural variant analysis and copy number variation detection.
For larger structural variants, short tandem repeat (STR) expansion genotyping, de novo assemblies and analysis of modified base calls please visit our LONG-READ WGS – select service.
For optional DNA isolation service, please refer to our DNA isolation guide.

Our solutions

HOW DOES IT WORK?

6 easy steps for a high quality WGS project

Study Design

Define sample number, data amount, starting material and data anlysis with our experts.

Sample Extraction

Samples can be sent for DNA extraction from a wide range of starting materials such as bacteria, cells, or tissue, and we have many years of experience performing high‑quality extractions.

Library preparation

We will perform library preparation according to the customer’s requirements, using either low or high amounts of starting material.

Sequencing

Freely choose the amount of data you need, or rely on the predefined data packages we have prepared for your WGS project.

Bioinformatics Analysis

From whole‑genome sequencing with de novo assembly to precise SNP and variant detection — we offer the solution that best matches your requirements.

Data consultation & Add-on services

Extended sample/data storage and data consultation services.

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Submit projects starting from just one sample and conveniently place your order online.

Two libraries for large genomes and free repeat prep in case of failure — for consistently higher data quality

Rigorous QC processes for every run. ISO 17025 certified lab.

Select a predefined product or freely choose your data volume, starting at 5 M read pairs.

Decades of experience in genomic services guarantee reliable performance.

Your data is delivered through our encrypted online platform.

DNA quantity is quality‑controlled prior to library preparation. Illumina‑compatible libraries are generated using Unique Dual Indexing for optimal data accuracy.

Sequencing is performed on the Illumina NovaSeq X+ system using the 2 × 150 bp run mode to ensure high-quality and high-throughput data generation.

You determine the sequencing depth that best fits your project.

With predefined products, the required data output is already calculated for you.
With our Genome Flex products, you can freely choose the exact data volume you need.

f you're unsure about how much coverage your project requires, here are general guidelines:

Germline/frequent variant analysis: 20-50x
Somatic/rare variants: 100-1000x
De novo assembly: 100-1000x

(Read length) × (Total number of reads) ÷ (Genome size).

Sequencing a 10 Mb genome with 20 million reads at 2 × 150 bp results in approximately 600× coverage.

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WGS of Human

Preparing 2 libraries for highest data quality

Choose between a premium and standard service.

WGS of Plants

Preparing 2 libraries for highest data quality.

Optional DNA extraction and bioinformatics analysis

WGS Flex

Free selection of data amount as multiples of 5 M read pairs.

Optional DNA extraction and bioinformatics analysis

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Sequence Quality Assessment
De novo assembly of reads
Annotation of draft assembly
Reporting & Consultation

Demo Report "De novo assembly"

Mapping against one reference
Detection of SNPs and InDels
Annotation of detected SNPs and InDels (using dbSNP)
Allocation of effects on protein level (using Ensembl)

More details about Variant analysis

We provide optional services such as structural variant analysis, copy number variation detection, tumor vs. normal and tumor-only (somatic) variant analysis to pinpoint genetic mutations in tumor samples, joint-genotyping to analyze multiple samples for shared genetic variations, and population genotyping to understand genetic diversity within specific groups.
Customizable BioIT solutions to tailor bioinformatics pipelines and tools to meet the unique needs of your research or clinical requirements
For larger structural variants, short tandem repeat (STR) expansion genotyping, and analysis of modified base calls please visit our long-read human WGS service.

NGS Prepaid Coupons make project planning easier by reducing administrative effort and securing consistent pricing ahead of time. They let you start sequencing whenever you’re ready — without waiting for new purchase approvals.

Available exclusively for Genome Seq Flex and Genome Seq Bacteria / Yeast / Fungi.

Find all essential information for preparing and shipping your samples, including packaging and labeling guidelines.

If you are sending material for DNA extraction, this section also outlines accepted sample types and the required input amounts.

Free barcodes are mandatory for sample processing to ensure correct tracking and handling of your material.

We also offer cost‑effective shipping options to make sending your samples as simple and affordable as possible.

We recommend purifying your DNA with commercially available kits based on DNA-binding beads or columns.

Samples that fail to meet the Incoming Quality Control (IQC) criteria (as defined on our website) may be canceled upon receipt of the IQC report, canceled with replacement samples sent, or processed further at the client’s own risk (in which case the read guarantee is no longer applicable).

If samples pass the Incoming Quality Control but subsequently fail the Library Quality Control, Eurofins will cover the costs of reprocessing the sample. If no sample material is available, we kindly request that you send us new starting material, if possible.

Depending on the type of virus or infectious material in your samples, we may be able to accept them. Eurofins can work with biosafety level L1 and L2 specimens. We do not accept samples with higher biosafety level than S2. GMOs are only accepted with S1 level. For RNA isolation service, please refer to our “Sample preparation and shipping guide for Extraction”. 

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 (see below). It leads you to our Order Tracking page where you can find all your samples and their current status.

Login to your Eurofins account with your e-mail address and password and click on “My Orders”, then on the icon next to your OrderID (see screenshot below).

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.

Yes, upon request, the service can be carried out under diagnostic conditions with ISO17025 certified workflows.

Long-read WGS

Order your UPS label or use our dropboxes for sample shipment. Please note that it is mandatory to use free NGS barcodes for sample shipment.

UPS labels / free barcodes Dropbox locations

How to retrieve my results

Below you can find instructions how to access your FTP folder or share your results with your colleagues.

How to access my FTP folder How to share results with my colleagues

WGS of Bacteria

Guaranteed coverage of 100x,

Sequencing using 2 x 150 bp run mode

Optional DNA extraction and bioinformatics analysis

WGS of Yeast

Guaranteed coverage of 70x,

Sequencing using 2 x 150 bp run mode

Optional DNA extraction and bioinformatics analysis

WGS of Fungi

Guaranteed coverage of 50x,

Sequencing using 2 x 150 bp run mode

Optional DNA extraction and bioinformatics analysis

WGS Essential

Only 100 ng genomic DNA required.

Free selection of data amount as multiples of 5 M read pairs.

WGS Flex
Free selection of data amount as multiples of 5 M read pairs.

Optional DNA extraction and bioinformatics analysis

Find Certificates here