BIO-DX & Genome Analysis
Genome Data Acquisition and Analysis for Industrial Organisms
From de novo genome assembly to whole-genome genotyping and variant analysis, we sequence industrial organisms mainly with long reads (PacBio HiFi) and work with you from experimental design through interpretation.
Service Overview
We sequence the genomes of industrial organisms and prepare data you can use for breeding, functional studies, and intellectual property (IP) protection. Long reads are our core approach, and we add short reads depending on the organism and the goal.
1. De novo genome assembly
We determine the genome of an organism that has no reference sequence.
Ideal for:
Decoding the genome of an organism with no reference sequence
Generating a genome sequence you can use in papers or patent applications
Protecting your biological resources as intellectual property
Key analyses: whole-genome assembly (draft, scaffold, or chromosome level, subject to consultation), gene prediction, and functional annotation
Options: a shortlist of candidate genome editing targets, additional annotation of non-coding RNAs or Gene Ontology (GO) terms, and a genome browser (JBrowse 2) and sequence search database (BLAST) set up for your data
2. Whole-genome genotyping and variant analysis
We detect variants and polymorphisms across the genome against a reference genome.
Ideal for:
Clarifying genetic differences between varieties or strains
Finding markers linked to valuable traits
Building the data foundation for marker-assisted selection (MAS) or genomic selection (GS)
Key analyses: detection of variants from single nucleotide variants (SNVs) to structural variants, population genetics, proposals for variety identification markers, variant detection in recombinant and genome-edited organisms, and variant comparison and time-course monitoring across strains and varieties
Options: support for polyploid genomes; locating an introduced gene or foreign sequence in the genome and counting its copies; and a genome browser (JBrowse 2) set up for your data
The PtBio Approach
Industrial organisms bring problems that standard pipelines cannot handle. Unlike model organisms, they often have a poor reference genome, sparse annotation, or a polyploid genome, and can be difficult to compare with related species.
PtBio addresses these problems through collaborative custom analysis. We start from your research goal and the biology of your organism and work with you from experimental design through analysis and interpretation.
What we resolve in the initial consultation
| Your challenge | What PtBio proposes |
|---|---|
| No reference genome, or a poor one | A sequencing strategy for your organism and de novo genome assembly |
| Not sure which analyses you need | An analysis menu matched to your research goal |
| Hard to interpret the data | Biological interpretation and recommended next steps |
| No bioinformatics staff in house | Ongoing analysis support and help setting up an analysis environment |
Why PtBio
| Strength | What it means for you |
|---|---|
| Collaborative custom analysis | One team supports you from experimental design to interpretation, tailored to your organism and goal |
| Joint research lab at Hiroshima University | We apply methods developed in joint research with the Laboratory of Bio-DX (Professor Hidemasa Bono, Graduate School of Integrated Sciences for Life) |
| Track record with industrial organisms | Many genome projects on industrial organisms with no reference genome |
| Read types chosen for your goal | We use long or short reads, depending on the analysis |
| One-stop service | One point of contact from DNA extraction through analysis, reporting, and setting up an analysis platform |
Technologies
| Method | Sequencing platform | Read type | Main use |
|---|---|---|---|
| Whole-genome sequencing | PacBio (HiFi) | Long reads (high accuracy, 15–20 kb) | Core technology for de novo assembly |
| Whole-genome sequencing and resequencing | Illumina | Short reads | Variant analysis and genotyping |
| GRAS-Di (low-cost genotyping) | Outsourced | Short reads | Phylogenetic and breeding data across many samples |
Detectable variant types
| Variant type | Short reads | Long reads |
|---|---|---|
| Single nucleotide variants (SNVs) | Yes | Yes |
| Insertions and deletions under 50 bp | Yes | Yes |
| Insertions and deletions of 50 bp or more | Limited | Yes |
| Inversions and translocations | Limited | Yes |
| Copy number variants (CNVs) | Limited | Yes |
Process
Contact us — We propose an analysis method that fits your goal.
Sample preparation & quality control (approx. 1–2 weeks) — Extraction of high-molecular-weight DNA, evaluation of DNA quality and purity, library preparation
Sequencing (approx. 3–4 weeks) — Long-read sequencing, short-read sequencing
Genome assembly & annotation (approx. 1–2 weeks) — de novo assembly, gap closing, gene prediction and functional annotation
Data analysis & report preparation (approx. 1–2 weeks) — Comparative genomic analysis, functional enrichment analysis, custom report preparation
In the initial consultation we ask about your research goal, organism, and budget, and propose a sequencing strategy and analysis plan. We can also propose an analysis environment your team can keep using after delivery.
Deliverables
You receive an analysis report that summarizes the results, and the full set of data behind it. We organize the data by analysis step in folders and deliver it on a hard drive or through cloud storage, in a form your team can reanalyze or hand to another provider.
Analysis report (PDF and HTML)
One document covers how we sequenced, what data we obtained, how we analyzed it, and what we found. Figures and tables come with biological interpretation and suggestions for what to examine next. Technical terms are explained in an appendix.
Included in every project
Raw sequencer output, with checksums so you can confirm the files are intact
Data volume and quality checks
A list of the software and databases we used, so the analysis can be reproduced later
When we assemble a new genome (de novo assembly)
The assembled genome sequence, the basis for patent filings, publications, and further analysis
An assessment of assembly quality: how contiguous it is, how complete the gene set is, and whether foreign sequences are present, shown in numbers and figures
Gene positions and structures, with the protein sequence each gene encodes
Predicted function for each gene from database matches, a starting point for finding genes of interest
Positions and proportions of repetitive sequences
When we compare varieties or strains, or call variants (genotyping, variant analysis)
Reads aligned to the reference genome, viewable in a genome browser
A list of detected variants: single-base changes, short insertions and deletions, and large structural changes
A filtered list of high-confidence variants annotated with the affected genes and likely effects (Excel), including whether genes of interest or known variants were confirmed
On request
A genome browser (JBrowse 2) set up for your data, with a walkthrough, so results can be checked on screen without a specialist
A sequence search database (BLAST) for locating one of your sequences in the genome
Additional annotation such as non-coding RNAs or Gene Ontology (GO) terms
Locating an introduced gene or foreign sequence in the genome and counting its copies
FAQ
Q: Which organisms can you analyze?
A: We have analyzed a wide range of species, mainly industrial organisms: plants, animals, microorganisms, and fungi. Genome size and ploidy differ by species, so we confirm feasibility and the approach in the initial consultation.
Q: We have no bioinformatics specialist in house. Is that a problem?
A: No. We support you from interpreting the results to recommending next steps.
Q: What is the typical timeline?
A: As a guide, a whole project takes 2–3 months from sample receipt to report delivery. The delivery times under Plans & Pricing cover the analysis step only. The timeline depends on the organism, data volume, and analysis scope, so we give a project-specific estimate in the initial consultation.
Q: How should we send samples?
A: Ship them frozen or refrigerated. We accept extracted DNA, or we can extract DNA from biological samples you send us.
Q: Can we get a cost estimate first?
A: Yes. We provide a rough estimate in the initial consultation.
Contact Us
For genome analysis inquiries and quotes, please contact us.