eDNA Metabarcoding
Identification of animals or plants using targeted barcoding
Targeted eDNA metabarcoding enables sensitive detection of vertebrate and metazoan taxa from environmental samples using established barcode loci such as COI and 12S, amplified as fragments and sequenced as overlapping paired-end reads on short-read sequencing platforms. This approach supports robust taxonomic assignment from complex samples while maintaining consistency with standard laboratory and bioinformatics workflows. eDNA metabarcoding supports ecological monitoring, conservation assessments, and regulatory reporting.
€ 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
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
• 75–300 bp
Depth
• ≥ 30 k 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
This streamlined, reproducible nf-core/ampliseq 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.