Mitochondrial Analyses
Analysis of mitochondrial sequence variation from NGS data
Mitochondrial DNA analysis enables characterisation of mitochondrial genomes and sequence variation from short-read sequencing data across human, animal, and plant samples. Depending on study design and data characteristics, analyses may focus on de novo reconstruction of mitochondrial genomes or reference-based assessment of sequence variation.
Processing mtDNA data can reveal mitochondrial haplotypes, sequence variants, and structural features relevant to population studies, evolutionary analysis, and disease or trait-associated research. Applying standardised, reproducible workflows ensures consistent handling of mitochondrial reads and supports reliable biological interpretation without 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
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 quality control summary of raw and processed sequencing data
mitochondrial_sequences
• Reconstructed or reference-aligned mitochondrial genome sequences, where applicable
variant_calls
• Identified mitochondrial sequence variants per sample
coverage_metrics.csv
• Summary of mitochondrial read depth and genome coverage per sample
summary_tables.csv
• High-level summaries of mitochondrial genome features or variant counts per sample
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
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
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, fully auditable 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.