Documentation Overview
Everything researchers, lab managers, and bioinformaticians need to know about the BioAnalysis.ca platform.
Platform Overview
How the system works, the three-step workflow, supported input formats, project management, and what makes BioAnalysis.ca different from existing solutions.
Read chapter →WGS Pipeline
Complete walkthrough of the whole-genome sequencing pipeline: quality control, species identification, genome assembly, gene annotation, AMR detection, and MLST typing.
Read chapter →16S/ITS Amplicon Pipeline
Microbiome community profiling: primer trimming, DADA2 denoising, taxonomy classification, alpha diversity, phylogenetic analysis, and functional prediction.
Read chapter →Reports & AI Interpretation
Interactive web reports, PDF export, AI-powered interpretation, comparative project reports, data visualization, and downloadable research data packages.
Read chapter →Technology & Infrastructure
Cloud architecture, security model, tool versions, reference databases, data handling, reproducibility, and the full technology stack powering the platform.
Read chapter →Why Researchers Choose BioAnalysis.ca
Zero Infrastructure
No HPC access, no Linux command line, no software installation. Upload your FASTQ files from any web browser and receive results automatically. Ideal for clinical labs, small research groups, and institutions without dedicated bioinformatics support.
Publication-Ready Output
Every report includes properly formatted tables, scientific charts with colorblind-safe palettes, complete methodology sections citing exact tool versions and database releases, and downloadable data packages suitable for journal supplementary materials.
AI-Powered Interpretation
AI reads your entire result set—taxonomy, diversity, AMR genes, assembly quality—and generates section-by-section interpretation in plain scientific English. Not a replacement for expert analysis, but a powerful first draft that saves hours of writing.
Cloud-Powered Compute
All analysis runs on scalable cloud infrastructure. Upload your files and the platform handles the rest — no local hardware, no software to install, no configuration needed.
Peer-Reviewed Tools
The pipeline uses exclusively peer-reviewed, publication-standard tools: DADA2, Kraken2, SPAdes, Bakta, AMRFinderPlus, MAFFT, FastTree, PICRUSt2—the same tools used by the leading microbiology research institutions worldwide.
Cloud Infrastructure
All analysis runs on scalable cloud infrastructure — your data is isolated per account and results are available as soon as the pipeline completes.
Supported Input Formats
| Format | Description | Pipelines |
|---|---|---|
.fastq.gz | Gzip-compressed FASTQ — the standard output from Illumina sequencers (MiSeq, NextSeq, NovaSeq) | WGS, 16S, ITS |
.fastq | Uncompressed FASTQ files | WGS, 16S, ITS |
| Paired-end (R1 + R2) | Two files per sample — forward and reverse reads. Recommended for 16S/ITS amplicon and WGS | WGS, 16S, ITS |
| Single-end | One file per sample — supported for both WGS and amplicon workflows | WGS, 16S, ITS |
Maximum file size: 10 GB per file. Illumina paired-end data is strongly recommended for best results. Files up to 10 GB are uploaded directly through the browser with resumable upload support.