Viral Metagenomics
Detection of viruses in shotgun sequencing data
Viral metagenomics can extend standard microbial analysis of shotgun sequencing data to detect viruses that are often missed in routine workflows. Checking your data for viral content can uncover biological insights, infections, contamination, or meaningful signals that affect interpretation and downstream decisions. Virome analyses adds confidence to your results, supports biosafety and regulatory needs, and can reveal unexpected findings without requiring new experiments.
€ 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
NCBI Submission
• FASTQ FTP upload to generate BioProject and Accession IDs
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 QC summary of raw versus cleaned sequencing reads
compositional_matrix.csv
• Clean-reads mapped to each taxon (rows) per sample (columns)
Requirements
Pipelines can be run on (i) newly generated datasets, (ii) publicly available metagenomes, or (iii) a combination of both, enabling comparative analyses across studies and environments.
This flexibility allows integration of novel samples with existing microbiome resources for broader context and reproducibility.
Input Format
• Paired- or single-end FASTQ (gzipped)
Read Length
• 50–150 bp
Depth
• ≥ 3 Mn reads
Optional Preprocessing
• Read repair – BBTools
• Host removal – Kraken2
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.
QC
• Tool(s): FastQC v0.12
• Purpose: Per-sample read quality analysis
Reporting
• Tool(s): MultiQC v1.31
• Purpose: Combined QC report
Trimming
• Tool(s): fastp v0.23
• Purpose: Adapter and low-quality trimming
Host Removal
• Tool(s): Kraken2 v2.0.8
• Purpose: Optional; host genome or taxonomy database required
Deduplication
• Tool(s): Clumpify v39.33
• Purpose: Duplicate read removal
Read Mapping
• Tool(s): Bowtie2
• Purpose: Short-read mapping to known databases
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
The streamlined, reproducible, nf-core/viralmetagenome and nf-core/viralrecon pipelines ensure 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.