Whole‑Genome Sequencing (WGS)

Comprehensive Whole‑Genome Sequencing (WGS) Services – From High‑Quality Library Preparation to In‑Depth Bioinformatic Analysis and Regulatory‑Grade Reporting

The adoption of whole‑genome sequencing (WGS) has transformed the landscape of microbial genomics, clinical diagnostics, food safety, pharmaceutical quality control, and environmental monitoring. Unlike targeted approaches that examine only a fraction of the genome, WGS provides a complete, unbiased view of the entire genetic blueprint of an organism, enabling the detection of all types of genetic variations – from single‑nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) to large structural variants (SVs) and plasmid content. This comprehensive resolution is indispensable for strain identification, outbreak investigation, antimicrobial resistance (AMR) profiling, virulence gene characterisation, and the verification of genetic stability in production strains. Regulatory bodies, including the US FDA, EMA, WHO, and national reference laboratories, increasingly recognise WGS as the gold‑standard method for molecular characterisation, and its use is now mandated or strongly recommended in many areas of public health and product safety. However, a successful WGS project is not merely a matter of running a sequencing instrument; it requires a carefully orchestrated workflow that integrates optimal sample preparation, high‑quality library construction, robust sequencing platforms (Illumina, Nanopore, or PacBio), and, crucially, state‑of‑the‑art bioinformatics pipelines for assembly, annotation, and advanced data interpretation. A poorly executed WGS project can lead to incomplete assemblies, missing variants, erroneous phylogenetic conclusions, and non‑compliant data, compromising the value of the analysis and undermining regulatory confidence. Our ISO/IEC 17025‑accredited and GMP‑compliant laboratory offers a fully integrated WGS platform, covering the entire spectrum from sample QC and library preparation to high‑throughput sequencing and comprehensive bioinformatics analysis – including de novo assembly, reference‑based mapping, variant calling, phylogenetic reconstruction, resistome and virulome profiling, and plasmid characterisation. We deliver quantitative, traceable genomic data, with full method validation, strict quality control, and expert interpretation, enabling you to obtain the complete genomic picture of your organisms, to trace outbreaks with single‑nucleotide resolution, and to meet the most stringent regulatory requirements with confidence.

1. The Scientific and Regulatory Imperative for Whole‑Genome Sequencing

WGS serves multiple critical purposes across diverse disciplines: (a) to provide the definitive identification of bacterial and fungal species at the strain level; (b) to characterise the complete antimicrobial resistance (AMR) profile by identifying all acquired resistance genes and chromosomal mutations; (c) to detect and characterise virulence factors and pathogenicity islands; (d) to enable high‑resolution epidemiological tracking by comparing isolates at the single‑nucleotide level; (e) to confirm the genetic stability and identity of production strains in biopharmaceutical manufacturing; (f) to support regulatory submissions for vaccine and therapeutic development; and (g) to discover novel genetic elements and understand the evolution of microbial populations. The choice of sequencing platform – whether short‑read (Illumina) for high‑accuracy variant calling, long‑read (Oxford Nanopore or PacBio) for complex structural variant detection and complete genome closure, or a hybrid approach – must be guided by the application, the organism, and the required level of resolution. Our service begins with a comprehensive consultation to define the optimal sequencing strategy for your project, ensuring both scientific rigor and regulatory compliance.

2. Our Comprehensive WGS Platform – From Sample to Highly Curated Report

We maintain a complete, validated WGS workflow, all performed in a dedicated genomics facility with stringent contamination controls, and using certified reference strains for quality assurance. Our portfolio includes:

2.1 Sample QC and Nucleic Acid Extraction – The Foundation of High‑Quality Data
We begin with a rigorous quality control (QC) step for all incoming samples, assessing the concentration, purity (A260/280, A260/230), and integrity of the extracted DNA using fluorometry and capillary electrophoresis (e.g., Qubit, BioAnalyzer, or TapeStation). We use validated extraction protocols (automated or manual) to obtain high‑molecular‑weight, pure DNA, free from inhibitors that could compromise the sequencing. We provide a detailed QC report, including the DNA yield, the fragment size distribution, and any recommendations for re‑extraction or sample processing.

2.2 Library Preparation – High‑Quality, Random‑Fragmented Libraries
We prepare sequencing libraries using validated, standardised protocols for both short‑read (Illumina) and long‑read (Nanopore, PacBio) platforms. For Illumina, we use a tagmentation‑based (e.g., Nextera) or ligation‑based method to generate libraries with a narrow insert size distribution (300‑600 bp) and with the appropriate indices for multiplexing. For Nanopore, we use the rapid barcoding or ligation sequencing kit to generate libraries suitable for long‑read sequencing. We incorporate internal controls and perform a library QC step (using a BioAnalyzer or Fragment Analyzer) to verify the library size and concentration before sequencing.

2.3 Sequencing Platforms – Illumina, Oxford Nanopore, and PacBio
We offer sequencing on the following platforms, selected based on your project requirements:

• Illumina (NovaSeq, NextSeq, MiSeq) – for high‑accuracy, short‑read sequencing with a low error rate (Q30 > 80%), providing a robust basis for SNP detection, gene calling, and MLST. We offer both paired‑end and single‑end sequencing, with a throughput of up to 600 Gb per run.
• Oxford Nanopore (PromethION, MinION) – for long‑read sequencing (up to 1 Mb or more), enabling the resolution of repetitive regions, the closure of complex genomes, and the direct detection of base modifications. We offer both rapid and ligation‑based library protocols.
• PacBio (Sequel, Revio) – for high‑fidelity (HiFi) long‑reads with > 99.9% accuracy, providing highly contiguous genome assemblies, and excellent for the detection of structural variants and the resolution of difficult‑to‑sequence regions.

2.4 Bioinformatic Processing – From Raw Reads to High‑Quality Genomes
Our bioinformatics pipeline includes the following steps, all executed using validated, open‑source and commercial software, and with regular pipeline validation and quality control:

• Read quality filtering and trimming – using tools such as Trimmomatic, fastp, or Porechop (for Nanopore), to remove adapters and low‑quality bases.
• De novo assembly – using assembly tools such as SPAdes, SKESA, Unicycler (hybrid assembly), or Flye (for long reads), to generate a high‑quality genome assembly. We provide both the contig‑level and, for long‑read data, the complete circularised chromosome and plasmid assemblies.
• Reference‑based mapping – using BWA‑MEM or Minimap2, to align the reads to a reference genome, enabling the detection of SNPs, small indels, and larger variants.
• Variant calling – using GATK, Samtools, or freebayes, to generate a comprehensive list of all genetic variants compared to the reference, with appropriate filtering and quality scoring.
• Genome annotation – using Prokka (for bacteria) or RAST, to generate a comprehensive annotation of all coding sequences, non‑coding RNAs, and other genomic features. We also provide custom annotation using the NCBI PGAP pipeline.
• Resistome analysis – using the Comprehensive Antibiotic Resistance Database (CARD), ResFinder, and AMRFinder, to identify all acquired resistance genes and chromosomal mutations associated with resistance.
• Virulence gene detection – using the Virulence Factor Database (VFDB) and the Victors database, to characterise the pathogenicity potential of the strain.
• MLST and serotyping – using the PubMLST database for multi‑locus sequence typing, and, for specific organisms, serotyping pipelines (e.g., SeqSero for Salmonella, SerotypeFinder for E. coli).
• Phylogenetic analysis – using the SNPhylo, RAxML, or IQ‑TREE software to construct a high‑resolution phylogenetic tree based on core‑genome SNPs or whole‑genome alignment, enabling the precise tracking of relatedness.

2.5 Data Interpretation and Reporting – Translating Genomics into Actionable Insights
Our reports are prepared by PhD‑level bioinformaticians and microbiologists and include:

• Genome statistics – including the assembly size, N50, the number of contigs, the GC content, and the completeness (using BUSCO or CheckM).
• Genome annotation – a list of all identified genes, including their function and their positions on the chromosome/plasmid.
• Antimicrobial resistance profile – a list of all acquired resistance genes and relevant mutations, with a clear interpretation of the expected phenotype (e.g., susceptible, intermediate, resistant).
• Virulence gene profile – a list of all identified virulence factors, with their functional classification.
• MLST and serotype – the definitive sequence type and serotype (where applicable).
• Phylogenetic tree – a high‑quality tree showing the relationship of your strain(s) to reference genomes or to other isolates in a database.
• Interpretative comments – providing a clear, contextual summary of the findings, the significance of the detected variants, and any recommendations for further analysis.

2.6 Method Validation and Regulatory Compliance – Full Documentation
We provide full method validation for your WGS project, including: (a) accuracy (by comparison with a reference genome); (b) precision (intra‑ and inter‑run reproducibility); (c) sensitivity (the detection limit for variants); and (d) specificity (the ability to correctly identify the organism). The validation report is structured to meet the requirements of regulatory bodies (e.g., FDA, EMA, or national authorities).

3. Advanced Capabilities – Long‑Read Hybrid Assemblies, Metagenomics, and Customised Analyses

For clients requiring the highest level of genomic characterisation, we offer a suite of customised, research‑grade services that go beyond the standard WGS pipeline:

3.1 Hybrid Assembly – Combining Short and Long Reads for Complete Genomes
We perform hybrid assembly by combining Illumina short reads (for high base‑level accuracy) with Oxford Nanopore or PacBio long reads (for scaffolding and resolving repeats). This yields the highest quality genome assembly, often producing a complete, circularised chromosome and all plasmids. This is essential for a definitive characterisation of the organism's genetic potential.

3.2 Metagenomic WGS – Direct Sequencing of Microbial Communities
We perform shotgun metagenomic sequencing on complex samples (e.g., environmental, clinical, or food samples) to characterise the entire microbial community. Our pipeline includes taxonomic classification (using Kraken2, MetaPhlAn, or Centrifuge), functional profiling (using HUMAnN3), and the detection of AMR and virulence genes directly from the metagenome.

3.3 Methylome and Epigenetic Analysis – Nanopore Direct DNA Methylation Detection
Using Oxford Nanopore data, we can detect and map DNA methylation patterns (e.g., 4mC, 5mC, 6mA) across the genome, providing insights into epigenetic regulation, gene expression, and the activity of restriction‑modification systems.

3.4 Plasmid Reconstruction and Characterisation
We perform a detailed plasmid analysis, including the detection of all replicon types, the identification of resistance and virulence genes carried on plasmids, and the reconstruction of plasmid structures (including the mobilisation and conjugation genes). This is essential for understanding the horizontal spread of AMR.

3.5 Phylogenetic and Population Genomics – Large‑Scale Comparative Studies
We can perform large‑scale comparative analyses, including the construction of core‑genome phylogenies, pangenome analyses (using ROARY or PanX), and the identification of core, accessory, and strain‑specific genes.

3.6 Customised Database Development – For Novel Organisms or Specific Markers
If your organism is not covered by standard databases, we can develop a custom reference database for that organism or a related group. We can also design and implement customised analysis pipelines for specific marker genes or genomic regions.

3.7 Data Review and Regulatory Submission Support
Our team of experienced genomic scientists and regulatory specialists can assist you in the interpretation of the genomic data, in the preparation of the required documentation for regulatory submissions, and in responding to queries from authorities. We provide a full data package, including the raw reads, the assemblies, the annotation files, and the analysis reports.

4. Data Integrity, Standardisation, and Comprehensive Reporting

All analyses are conducted under a strict quality management system that includes the use of certified reference strains, routine positive and negative controls, and participation in proficiency testing schemes (e.g., the FDA’s GenomeTrakr, or the UK NEQAS). Our reports provide:

• Full method description – detailing the sample preparation, the library preparation method, the sequencing platform, the bioinformatics pipeline, and the data analysis parameters.
• Detailed results – including the genome assembly, the annotation, the resistance and virulence gene lists, the MLST/serotype, and the phylogenetic tree.
• Quality control data – including the read quality scores, the depth of coverage, the assembly completeness, and the results of the concurrent controls.
• Graphical outputs – including the genome circular plots, the coverage histograms, the phylogenetic tree, and any relevant heatmaps or visualisations.
• Interpretative comments – by our senior genomic scientists, providing an assessment of the genomic findings, the significance of the detected variants, and any recommendations for further analysis.

Our reports are structured to meet the requirements of regulatory audits, customer inspections, and internal quality assurance.

Turnaround times: 1‑2 weeks for standard Illumina WGS (including bioinformatics), 2‑3 weeks for hybrid assemblies and complex analyses, and 3‑4 weeks for metagenomic and custom‑pipeline projects. Express services are available for urgent cases.

5. Why Choose Our Laboratory for Whole‑Genome Sequencing

We are one of the few laboratories that hold ISO/IEC 17025 accreditation and GMP compliance for WGS services, covering the full range of sequencing platforms and bioinformatics analyses. Our integrated infrastructure combines state‑of‑the‑art sequencing instruments, automated library preparation systems, and a powerful bioinformatics cluster with validated pipelines – enabling cross‑verification of results and a consistent, high‑quality output. Our team comprises PhD‑level molecular biologists, bioinformaticians, and genomic scientists with extensive experience in method development, validation, and regulatory submissions, and we have a proven track record of supporting public health, food safety, and pharmaceutical quality‑control programmes.

We offer unparalleled flexibility: we accept all types of microbial samples – from pure cultures, food, water, clinical specimens, and environmental swabs – and we provide customised sequencing strategies to meet your specific organism, application, and budget requirements. Our secure online portal enables real‑time tracking, access to raw data, and downloadable certificates of analysis.

Our modular pricing ensures cost‑effectiveness: you select the level of analysis – from a simple identification to a full genomic characterisation – with discounts for routine monitoring programmes and bulk submissions. We also provide training, method transfer, and technical consultancy to help you build or strengthen your internal WGS capabilities.

With a proven history of serving over 80 clients in the food, pharmaceutical, and public health sectors, we have enabled our partners to achieve definitive strain characterisation, trace contamination sources, and ensure the genetic integrity of their products. We invite you to leverage our expertise for your whole‑genome sequencing needs.

Contact our technical experts today to discuss your sample types, target organisms, and specific investigative or quality‑assurance objectives. We will design a tailored sequencing plan and provide a detailed proposal within one business day.