What Is BioAnalysis.ca?
BioAnalysis.ca is a fully automated, cloud-based bioinformatics platform designed for researchers who need to analyze bacterial genomic data without maintaining their own computational infrastructure. The platform accepts raw sequencing data (FASTQ files) from Illumina sequencers and performs end-to-end analysis using peer-reviewed, publication-standard bioinformatics tools.
The platform supports two distinct analysis modes:
🧬 Whole-Genome Sequencing (WGS)
For pure bacterial isolates. Performs quality control, species identification, de novo genome assembly, gene annotation, antimicrobial resistance (AMR) gene detection, and multi-locus sequence typing (MLST). Ideal for clinical isolate characterization, outbreak investigation, and genomic surveillance.
🔬 16S/ITS Amplicon Analysis
For microbiome community profiling. Performs primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy classification against SILVA v138.2 (16S) or UNITE v9.0 (ITS), alpha diversity metrics, phylogenetic tree construction, and functional prediction via PICRUSt2.
The Three-Step Workflow
BioAnalysis.ca was designed around the principle that bioinformatics should not be the bottleneck in microbiology research. The entire process—from raw sequencing data to interpreted results—requires three actions from the user:
Step 1: Upload FASTQ Files
Drag and drop .fastq.gz or .fastq files directly in the browser. Select the analysis type (WGS or 16S/ITS), choose the analysis tier, and optionally assign the sample to a project for comparative analysis later. Paired-end and single-end reads are both supported. Files must be under 1 GB each. You can upload up to 200 files (100 samples) per batch submission.
Step 2: Automated Analysis
Once uploaded, the platform runs the full bioinformatics pipeline automatically. Each step is tracked in real time — the dashboard shows exactly which tool is running, what percentage is complete, and how long the analysis has been running. No user intervention is needed during this phase.
Step 3: Explore Results
When the pipeline completes, results are available in two formats: an interactive web report accessible from any browser (with tooltips, hoverable charts, and dynamic visualizations) and a downloadable PDF formatted for printing and archiving. An AI interpretation section provides professional scientific commentary on every result section.
Dashboard & Job Management
After logging in, researchers see a unified dashboard that displays all their analyses in a single view:
| Column | Description |
|---|---|
| Sample | Original filename and file size of the uploaded FASTQ data |
| Type | Analysis type badge: 🧬 WGS, 🔬 16S, or 🍄 ITS |
| Status | Current state: Queued, Running (with spinner), Completed (✓), or Failed (✕) |
| Progress | Visual progress bar with percentage and current pipeline step label (e.g., "Taxonomy Classification") |
| Species | Primary organism identified — dominant species (WGS) or dominant genus (amplicon) |
| Submitted / Completed | Timestamps for job creation and completion |
| Duration | Total wall-clock time from start to finish |
The dashboard auto-refreshes every 10 seconds while jobs are running, so researchers can monitor progress in real time without manually reloading. Clicking any row navigates directly to that job's detailed report page.
Project System & Comparative Analysis
Samples can be grouped into projects for cross-sample comparison. This is particularly powerful for amplicon studies where researchers are comparing microbiome communities across conditions, time points, or treatment groups.
Projects require a minimum of 2 samples and support up to 100 samples per project. When a project contains multiple completed amplicon analyses, the platform generates a comparative project report that includes:
- Alpha Diversity Comparison — Shannon, Simpson, Chao1, Observed ASVs, and Faith's PD displayed as animated bar charts with a project-mean reference line for instant visual benchmarking
- Stacked Phylum Composition — side-by-side phylum-level composition bars for all samples, color-coded with a consistent palette
- Richness vs. Evenness Scatter Plot — Observed ASVs plotted against Shannon index to identify outlier samples
- Bray-Curtis Dissimilarity Matrix — pairwise compositional distance heatmap computed from genus-level abundances
- Core Microbiome Analysis — genera classified as core (>80% prevalence), common (30-80%), or rare (<30%) across all project samples
- Sample Overview Table — all diversity metrics, dominant genera, and read counts in a single sortable table
Typical Processing Times
Processing times depend on input file size and sequencing depth. Times shown are for typical Illumina MiSeq paired-end datasets. All pipelines include AI interpretation, which adds approximately 30-60 seconds to the total time.
Analysis Tiers
WGS Tiers
| Tier | Steps Included | Typical Use Case |
|---|---|---|
| Basic | QC (Fastp) → Species ID (Kraken2) → AI Interpretation → Report | Quick species identification from an isolate |
| Standard | Basic + ConFindr contamination check → SPAdes assembly → QUAST → Bakta annotation → MLST typing | Full genome characterization |
| Advanced | Standard + AMRFinderPlus AMR/virulence detection → Research Data Package (ZIP) | Clinical/AMR surveillance, publication-grade output |
Amplicon Tiers
| Tier | Steps Included | Typical Use Case |
|---|---|---|
| Amplicon Basic | Cutadapt primer trimming → DADA2 denoising → SILVA/UNITE taxonomy → Composition charts → AI Interpretation → Report | Quick microbiome profiling — "what's in my sample?" |
| Amplicon Complete | Basic + MAFFT/FastTree phylogeny → Alpha diversity (Shannon, Simpson, Chao1, Faith's PD, rarefaction) → PICRUSt2 functional prediction → Research Data Package | Full microbiome study with diversity metrics and functional analysis |