Mitochondrial Assembly
Assembly of mitochondrial sequences from NGS data
Mitochondrial DNA analysis is performed using MitoZ to assemble mitochondrial genomes from short-read sequencing data across human, animal, and plant samples. The workflow focuses on de novo reconstruction of mitochondrial sequences and generation of standard annotation outputs based on the input data.
Processing mtDNA data with MitoZ produces assembled mitochondrial contigs along with basic gene annotations and summary metrics describing the recovered sequence content. Output typically includes FASTA and GFF files representing the draft mitogenome and associated features.
Applying a standardised, reproducible workflow ensures consistent handling of mitochondrial reads and generation of straightforward assembly deliverables, without additional downstream interpretation or custom analysis.
€ 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.
Mitochondrial sequences
• Assembled mitochondrial genome sequences
Annotated genomes
• Genbank format mitochondrial genome features
Requirements
Pipelines can be run on (i) newly generated datasets, (ii) publicly available datasets, or (iii) a combination of both, enabling comparative analyses across studies and environments.
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
• ≥ 1 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.
MitoZ log
-
Text log of the MitoZ pipeline, including parameters
Assembly Options
-
Megahit (default), Spades, or Mitoassemble
Quality Control
-
Return of Fastp cleaned reads, if requested
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.