Human WGS
Comprehensive genomic variation analysis using WGS
Whole genome sequencing (WGS) enables comprehensive analysis of genetic variation across the entire human genome, providing a high-resolution view of single nucleotide variants, insertions/deletions, structural variants, and copy number changes. Using standardised, reproducible workflows such as nf-core/sarek, raw sequencing reads are processed through alignment, variant calling, and annotation to generate high-confidence genomic profiles suitable for research interpretation.
Robust quality control at each stage ensures data integrity and comparability across samples, supporting downstream analyses such as variant prioritisation, population comparisons, and genotype–phenotype association studies. Re-analysis of existing WGS datasets using updated pipelines and reference databases can further enhance variant detection sensitivity and improve biological interpretation without the need for additional sequencing.
€ Priced based on project discussion(s). Get in touch:
Details
This service is for the FASTQ data processing, QC reports, and minimal biological or statistical interpretation.
Optional add-ons such as figure preparation, or data upload to public repositories, are available on request.
Project Setup
• Includes project discussions and data transfers
Analysis per Sample
• Suitable for 1 to >100 samples
Figures & Statistics
• Composition, diversity, statistical test, and differential abundance
Video Discussions – n=3
• Kick-off, update, and wrap-up calls
Turnaround Time – 2–3 weeks
• Queue and project size dependent
Delivery – Dropbox / FileZilla
• Data retained for 30 days
Deliverables
All files are shared via secure, GDPR-compliant data transfers.
Data upload and release will be organised via Dropbox or Filezilla.
Compute resources are provided by an Irish-based cloud computing provider, CloudCIX.
multiqc_report.html
• Aggregated quality control summary of raw sequencing data, alignment metrics, and variant calling performance
aligned_reads.cram
• Reference-aligned sequencing reads in compressed CRAM format for downstream analysis and archiving
aligned_reads.crai
• Index file for rapid access to CRAM alignments
variants.vcf.gz
• High-confidence small variant calls (SNVs and indels) across the genome
variants.tbi
• Index file for compressed VCF enabling fast querying
Requirements
Pipelines can be run on newly generated data or publicly available data.
This flexibility allows integration of novel samples with existing resources for broader context and reproducibility.
Input Format
• Paired- or single-end FASTQ (gzipped)
Read Length
• 50–150 bp
Depth
• ≥ 30 Mn reads
Optional Preprocessing
• Read repair – BBTools
Accepted Platforms
• Illumina, MGI, Element Biosciences, Ultima Genomics
Technical
All analyses are executed within isolated Conda environments, ensuring full reproducibility and dependency control across runs.
Each tool and database version is tracked, guaranteeing consistent results between projects and over time.
nf-core/sarek
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Revision 3.5.0 (https://nf-co.re/sarek)
Workflow
Client data are transferred securely to BioFigR via Dropbox/Filezilla and processed on CloudCIX infrastructure using rsync. All transfers occur within GDPR-compliant environments, with optional deposition to NCBI via FTP only upon client approval. No data are shared or stored beyond the agreed workflow stages.
Contact BioFigR
This streamlined, reproducible pipeline ensures data integrity from upload to analysis. BioFigR provides transparent, compliant handling at every stage—so clients can focus on results, not logistics.
Contact BioFigR with the number of samples and reads per sample to receive a quotation, or to discuss project requirements.