Illumina Whole Genome Sequencing of pure bacterial strains under ISO&GMP compliance, including variant calling against the strain’s reference genome.
Our ISO & GMP-compliant Illumina Bacterial Whole Genome Sequencing is a genomic analysis service that uses Illumina next-generation sequencing technology to identify and analyze the complete DNA sequence of bacterial organisms under strict quality and processing standards. This service includes DNA extraction, library preparation, normalization and pooling, sequencing and bioinformatics analysis, as well as several QC steps through the whole process. A comprehensive ISO & GMP-compliant report is generated as the final deliverable along with the raw sequencing data. This service enables the characterization of bacterial strains, by, for example, detecting mutations or antimicrobial resistance genes. Thanks to its validated workflows and thorough quality assurance, it can also serve to support research, product safety or regulatory compliance.
This service is fundamentally designed to aid pharmaceutical companies, biotechnology firms, clinical research organizations, healthcare institutions, and food or environmental testing laboratories that require highly accurate bacterial genomic data. The service is especially valuable for projects involving microbial characterization of production strains, antimicrobial resistance analysis, food safety, contamination monitoring, or simply regulatory research. Baseclear’s ISO & GMP-compliant and standardized sequencing workflow helps overcome challenges related to bacterial identification or regulatory compliance submissions by delivering precise, reproducible, and high-quality sequencing results.
This service uses a fully validated next-generation sequencing (NGS) workflow performed under ISO&GMP-compliant laboratory conditions. The methodology begins with an automated bacterial DNA extraction using a Kingfisher Flex Purification System and it is followed by a gDNA QC step that employs fluorometric quantitation. Then, the gDNA is library prepped using Nextera Flex library preparation, which enables a superior coverage uniformity and reduced bias compared to other Illumina libraries. Subsequently, the library quality is verified during the Library QC using the Fragment Analyzer and automated normalization and pooling occurs, generating the final pool for the sequencing. Before loading, an additional Pool QC is performed and then, the samples are paired-end sequenced using the Illumina high-throughput sequencing platform, NovaSeq 6000. Sequencing data is processed through our validated bioinformatics pipelines for variant calling or SNP detection using the genome reference provided by the costumer. The entire workflow is supported by our validated LIMS and follows strict quality control procedures, including sample traceability, contamination monitoring, and data verification to ensure accurate, reproducible, and regulatory-ready results.
Clients receive a comprehensive package of sequencing and variant analysis deliverables. Results include quality-controlled sequencing data, genome alignment files, detailed variant call tables describing identified SNPs, insertions, and deletions, and summary reports outlining variant frequencies, genomic locations, and quality metrics. The final report documents the analytical methods used, validation status of the workflow, and interpretation of the results, providing clients with actionable genomic insights to support research, development, manufacturing, and regulatory decision-making.
Together, we discuss your viral system, study goals, and variant detection requirements. Our team helps determine the most suitable sequencing and analysis strategy based on your research, development, or quality-control objectives.
You provide viral material together with the relevant project information and reference genome details. BaseClear performs the required quality assessments and keeps you informed throughout the project lifecycle.
Your samples undergo whole genome sequencing using validated Illumina workflows designed for high-quality viral genome characterization. Sequencing data are generated with sufficient coverage to support reliable variant detection across the viral genome.
BaseClear analyzes the sequencing data using validated bioinformatics pipelines to identify SNPs, insertions, and deletions relative to the reference genome. Quality metrics and analytical controls are applied to ensure accurate and reproducible results.
You receive a comprehensive report containing identified variants, sequencing quality metrics, genome analysis results, and supporting data files. The results provide clear genomic insights to support research, process development, manufacturing, and regulatory decision-making.
Genomics and sequencing projects completed
Years of sequencing and genomics expertise
Validated molecular analysis workflows
Cell culture samples analysed
The workflow is highly scalable. Every step of the process uses a 96-well plate and more than 300 samples can fit within a pool. In the past, we have sequenced projects of more than 2000 samples.
Every step of the process includes positive and negative controls. We use the negative controls to monitor possible contaminations at each one of the QC steps.
During our QC steps we evaluate that there is sufficient input for the next step and that the quality of the sample are within Illumina specifications. For example, during the library prep we verify, among others, that the length of the library is compatible with the sequencing platform and that the stablished threshold for the percentage of adapter dimer is meet, which reflects library quality.
It can. However, for large indels or structural variants, we advise complementing this Illumina service with ONT sequencing. ONT technologies better capture mutations bigger than 50 bp.
For detection of common mutations (>30%), we provide an average coverage depth of 150-200x with a guarantee of ≥20x for 90% of the genome length. For rarer mutations, we use 1000x coverage.
The workflow is highly scalable. Every step of the process uses a 96-well plate and more than 300 samples can fit within pool. In the past, we have sequenced projects of more than 2000 samples.
We do and the de novo genome assembly pipeline is also validated.
Detect mycoplasma contamination in cell cultures using sensitive molecular detection methods.
High-accuracy DNA sequencing for PCR products, plasmids, and targeted genetic regions.
Quantify the residual host cell DNA in your samples using digital PCR technology.
Speak with our experts to discuss your cell line identification project. We will help you determine the appropriate analysis approach and provide reliable sequencing results to support your research and quality control workflows.
