Pipelines Metabarcoding • 16s • 18s • its

Turn Raw Reads into Actionable Insights in Minutes

Self-service bioinformatics for microbiome researchers. Upload your FASTQ files, choose your pipeline, and explore interactive reports - no command line required.

Analyze My Data See How It Works
No credit card required Results in hours Enterprise Grade Security
Why Silicobiome

Everything You Need for Amplicon Analysis

From raw sequencing data to publication-ready figures

FASTQ

Drag-and-Drop Upload

Drop FASTQ files directly in the browser. Paired-end, multiplexed, and gzip-compressed archives — all handled automatically.

CONFIG

Custom Pipelines

Customize your bioinformatics pipeline by specifying your amplicon markers, adapters, and primers. All downstream parameters are optimized automatically for your chosen assay.

VIZ

Quality Reports

Get full QIIME 2 - compatible outputs: alpha/beta diversity, PCoA plots, taxonomy barplots, phylogenetic trees, feature tables, and QC reports.

GDPR

Enterprise Security

Dedicated on-premise infrastructure. AES-256 encryption. GDPR compliant. Auto-deletion policies. Your data never leaves our secure environment.

DB

SILVA / UNITE

Full taxonomy assignment using the latest reference databases for bacteria, eukaryotes, and fungi across all amplicon types.

FAST

Results in < 2 Hours

Our own dedicated scalable infrastructure means most standard datasets are fully processed in under 2 hours.

How it works

From Raw Reads to Results in 5 Steps

1
FASTQ • FQ.GZ

Import Your Data

Drag & drop FASTQ files. We handle the rest.

2
16S • 18S • ITS

Configure Pipeline

Choose 16S, 18S or ITS. Set adapters and trimmers we optimize the rest.

3
< 2 Hours

Run the Pipeline

Our dedicated infrastructure auto-scales to process your dataset in under 2 hours.

4
FLEXIBLE

Pay Per Run

No subscription needed. Pay only for the analyses you run. Enterprise flat-rate plans also available.

5
INTERACTIVE

Explore Results

Interactive diversity plots, taxa bar charts, PCoA ordinations, and rarefaction curves — all downloadable and shareable.

Try it now

Run Your First Pipeline Without Signing Up

Upload your FASTQs, pick your markers and watch Silicobiome deliver diversity results.

No Account Required
Pay Only When Results Available
Instant Price Calculation
See Output Metrics Immediately
Analysis Pipelines

Purpose-Built for Every Amplicon Type

Choose from validated pipelines for 16S, 18S, and ITS amplicon sequencing. Each is optimized for its target marker gene and reference database.

Bacteria & Archaea

16S rRNA Pipeline

The gold standard for bacterial community profiling. Our pipeline supports V3-V4, with custom primer pairs and DADA2-based ASV inference and SILVA taxonomy.

Reference Databases
SILVA
Typical Turnaround
~1 hour (10 samples)
Pipeline Steps
  1. 01Quality Control (FastQC + MultiQC)
  2. 02Primer Trimming (Cutadapt)
  3. 03Merging paired reads (VSearch)
  4. 04Parameter Estimation (Figaro)
  5. 05Filtering and Denoising (DADA2)
  6. 06Taxonomy Classification (SILVA & NCBI)
  7. 07Alignment and Phylogeny
  8. 08Diversity Analysis
Pricing

Scale With Your Research

No hidden fees. Pay per sample, or choose a subscription plan for lower per-analysis costs and priority turnaround.

Pay-as-you-go Recommended

Configure only what you need and approve the quote before anything starts.

From €5 / sample

Price calculated at configuration

Costs depend on pipeline type, number of samples, reference databases, and custom classifiers. You see the full quote before launching the run.

Configure & Get Price
Price depends on
Pipeline type 16S - 18S - ITS
Number of samples 1 - unlimited
Reference database SILVA - UNITE
Analysis depth Diversity - Taxonomy - Custom
Exact quote shown before pipeline starts. Pay only on completion.
Or choose a subscription plan - ideal for teams with recurring analysis volume
Most popular
Researcher

For individual researchers and small labs running projects every month.

€49 / month
Contact Sales
  • 25 samples per month
  • 16S, 18S and ITS pipelines
  • No additional costs for custom classifiers
  • Publication-ready exports
  • Email support
Lab

For growing labs with high throughput needs and repeatable workflows.

€499 / month
Contact Sales
  • 275 samples per month
  • 16S, 18S and ITS pipelines
  • No additional costs for custom classifiers
  • Priority in queue for processing
  • Publication-ready exports
  • Email and On-Call support
Institution

For core facilities and multi-team environments with advanced compliance needs.

Custom
Contact Sales
  • Unlimited samples
  • 16S, 18S and ITS pipelines
  • No additional costs for custom classifiers
  • Even more priority in queue for processing
  • Publication-ready exports
  • Email and On-Call support
  • Dedicated support engineer
Subscriptions Plans - Available starting on the 15th of September

Common Questions

Quick answers about data ownership, turnaround time, supported formats, and deployment options before you start your analysis.

Talk With Us
Who owns the data I upload?
You retain full ownership of all uploaded sequencing data, metadata, and generated outputs. Silicobiome processes the files only to execute the selected analyses.
How fast will I get my results?
Most standard 16S, 18S, and ITS runs are completed in under 2 hours, with turnaround depending on sample count, pipeline complexity and availability of our infrastructure.
What input formats are supported?
Silicobiome supports FASTQ, FQ, and gzip-compressed FASTQ archives for samples. .qza is suported for custom classifiers.
Can I customize the analysis parameters?
Yes. You can configure adapters, primers and custom classifiers before launching a run. Downstream analysis options are optimized for your chosen assay.
What happens if a pipeline fails?
If a pipeline fails to process your data you will be able to reconfigure the run or use our support team to help you process it again. No cost when the pipeline fails, only pay when results are available.
Can I deploy Silicobiome on-premise?
No. Silicobiome is a proprietary technology created by STABVIDA and is only available as a service.

Ready to Accelerate Your Microbiome Research?

Join hundreds of researchers using Silicobiome to turn raw sequencing data into actionable insights.

Start Analysing
No credit card required No account required Pay only when results are available