Bacterial whole-genome sequencing analysis
Upload FASTQ files from a pure bacterial isolate and get species identification, a de novo assembly, gene annotation, MLST type and antimicrobial resistance genes in one report. From $15 CAD per sample.
The bacterial WGS pipeline
Established tools for bacterial genomics, run automatically from raw reads to annotated genome.
Quality control (fastp v1.1.0)
Read filtering, adapter trimming, quality and GC content profiles.
Contamination check (ConFindr)
Detects intra- and cross-species contamination, so a mixed culture is caught before it skews the assembly.
Species ID (Kraken2 v2.17.1 + Bracken)
Taxonomic classification of reads with species-level abundance re-estimation and confidence.
Assembly (SPAdes v3.15 + QUAST)
De novo genome assembly with N50, contig count, genome size and completeness metrics.
Annotation (Bakta v1.12.0)
Coding sequences, rRNA, tRNA and functional categories across the genome.
MLST (mlst v2.33.1)
Multi-locus sequence typing for epidemiology and strain tracking.
AMR (AMRFinderPlus v4.2.7)
Antimicrobial resistance, stress response and virulence genes from the NCBI curated reference database.
WGS analysis pricing
Per isolate, in Canadian dollars, with no subscription.
Basic Report
- Quality control (fastp)
- Species identification (Kraken2 + Bracken)
- AI-assisted interpretation
- PDF and interactive web report
Standard Report
- Everything in Basic
- Contamination check (ConFindr)
- Genome assembly (SPAdes + QUAST)
- Gene annotation (Bakta)
- MLST typing
- Multi-sample projects
Advanced Report
- Everything in Standard
- AMR gene detection (AMRFinderPlus)
- Resistance mechanism report
- Publication-ready charts
- Research data package (ZIP)
Bacterial WGS FAQ
What is the difference between WGS and 16S analysis?
WGS sequences the entire genome of one pure bacterial isolate, so it can identify the species precisely, assemble the genome and find resistance genes. 16S sequencing reads one marker gene from every bacterium in a mixed community, so it profiles who is present but not their full gene content.
What input does bacterial WGS analysis need?
Illumina short-read FASTQ files, paired-end or single-end, from a single bacterial isolate grown in pure culture. Mixed or contaminated cultures are flagged by the ConFindr contamination check.
Can the WGS results be used for clinical decisions?
No. Reports are for research use only. Resistance genes detected by AMRFinderPlus indicate genetic potential and must be confirmed with phenotypic antimicrobial susceptibility testing.
Analyze your bacterial isolate
Your first analyses are free, with no credit card. Upload FASTQ files and get an annotated genome and AMR report.