Short-Read Whole Genome Sequencing (WGS)

Precision Short‑Read Whole Genome Sequencing

WGS Bacteria, Fungi, Yeast

WGS Human, Mammals, Plants, Larger Eukaryotes

De novo assembly or comprehensive SNP/variant analysis?

Need something else?

NGS Prepaid Coupons

NGS Sample Submission

Free Barcodes, UPS Labels, Dropbox usage

Key Benefits of Our Whole Genome Sequencing Services

Quality is important for us at Eurofins

Product specifications

Additional services & important links

Quick Start

Reliability

Accuracy

Flexibility

Expertise

Secure data

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 all sample types, including humans, animals, plants, yeast, other eukaryotes, bacteria, 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

De novo and 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

Our solutions

HOW DOES IT WORK?

6 easy steps for a high quality WGS project

Study Design

Define sample numbers, data output, starting material, and bioinformatics requirements together with our experts to ensure your project begins with the optimal setup.

Sample Extraction

Send us your samples for DNA extraction from a wide range of starting materials, including bacteria, cells, and tissue. Our long-standing expertise ensures reliable, high‑quality extractions.

Library preparation

We perform library preparation according to your project needs, using either low or high input amounts to deliver optimal results.

Sequencing

Choose freely how much data each sample should receive, or select from our predefined data packages tailored for whole‑genome sequencing projects.

Bioinformatics Analysis

From de novo assembly to accurate SNP and variant identification, we provide the bioinformatics solution that best fits your research goals.

Add-on services

Optional extended sample or data storage, as well as expert data consultation services, are available to complement your project.

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Choose WGS Bacteria, Yeast, or Fungi for guaranteed coverage at organism-specific depths, opt for WGS Flex if different coverage is required, or select WGS Essential for low-input projects needing minimal DNA with flexible data output.

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WGS Human offers optimized dual-library preparation with standard or premium service options, while WGS Flex provides customizable data output for mammals, plants, and other larger eukaryotic genomes—including human—ideal when flexibility is required.

WGS Human

Two libraries per sample for low duplication and GC-bias–free coverage

Optional DNA extraction and bioinformatics analysis

Choose between a premium (30x coverage guaranteed) and standard (30x on average) service.

WGS Flex 2

Ideal for large mammal and eukaryotic genomes, including plants and customizable human projects

Flexible data output selectable in increments of 5 M read pairs

Two libraries per sample for low duplication and GC-bias–free coverage

Optional DNA extraction and bioinformatics analysis

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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.

Predefined packages for bacteria, yeast, fungi, and human guarantee the recommended data output for your project.
With WGS Flex, you can freely choose the exact data volumen you need.

If 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.

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

Demo Report "De novo assembly"

Mapping against one reference genome
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 solutions to adapt bioinformatics pipelines and tools to your research needs
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 WGS Flex and WGS 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.

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

Two libraries for large genomes and free repeat prep (premium) 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.

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

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.

For our Standard Services, we do not guarantee a specific coverage level or a minimum amount of data. These offerings are designed as highly streamlined workflows without individual project supervision or data‑yield assurance.

A properly submitted high‑quality sample will typically achieve the read output specified in the product description. However, because samples and biological materials can vary, insufficient coverage can occasionally occur.

If you require guaranteed data output, dedicated project oversight, and iterative adjustments to ensure the target coverage is reached, we recommend choosing our Premium Service>>, where a project manager actively monitors your project and ensures delivery of the agreed data volume.

Our standard products are designed to deliver high‑quality results as quickly and cost‑efficiently as possible. To achieve this, these workflows run in highly optimized, streamlined processes that do not allow for individual project supervision or iterative adjustments if a specific data yield is not reached.
For projects that require guaranteed data output, dedicated guidance, and active optimization, we offer our Premium Service. Here, a specialized project manager oversees your entire workflow and ensures that the agreed data volume is reliably achieved.

For guaranteed data output, simply order through our Premium page >> —where you can flexibly choose your desired data volume and the ideal product for your available starting material for bacteria, yeast, or fungi.

Sample shipment

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 Bacteria

Guaranteed 100x coverage (for genomes up to 9 Mb)

Sequencing using 2 x 150 bp run mode

Optional DNA extraction and bioinformatics analysis

WGS Yeast

Guaranteed 55x coverage

Sequencing using 2 x 150 bp run mode

Optional DNA extraction and bioinformatics analysis

WGS Fungi

Guaranteed 50x coverage

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

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