Genome assembly & typing
De novo and reference assembly with QC, plus MLST, cgMLST, and serotyping to place isolates in a standard nomenclature.
Research Area
Microbiology & Infectious Disease
Pathogens evolve in real time—acquiring resistance, jumping hosts, and seeding outbreaks in weeks. Genomics is how we keep up. We bring the computational tools that track them: genome assembly and typing, resistance profiling, outbreak phylogenetics, and viral lineage assignment, for research and surveillance.
Bacterial & viral WGS
AMR & typing
Outbreak phylogenetics
Research & surveillance · not clinical
Illustrative sample output
cluster A
cluster B
cluster C
Overview
Reading pathogen genomes to track and understand disease
Infectious-disease genomics moves fast and at scale. A single outbreak can generate thousands of isolate genomes; resistance and virulence are encoded across chromosomes, plasmids, and mobile elements; and the questions that matter—who is related to whom, what is spreading, what is resistant—depend on resolving differences of just a handful of SNPs. Standard pipelines rarely handle the typing schemes, curated resistance databases, and phylogenetic methods this work requires.
We bring those methods to your pathogen data. From assembly, typing, and antimicrobial-resistance profiling to core-genome SNP analysis, outbreak phylogenetics, phylodynamics, and viral lineage assignment, we apply established, community-standard tools against trusted reference databases—and return results documented for reproducibility. This is research, public-health, and surveillance work: it is not a clinical diagnostic or susceptibility service, which stays with accredited laboratories.
Applications
What we analyse in pathogen genomics
The computational analyses that turn pathogen sequence into surveillance and biology—from assembly and resistance to outbreak phylogenetics.
Antimicrobial resistance
Detection of resistance genes and mutations against curated databases—genotype-based surveillance, not a clinical susceptibility test.
Outbreak & genomic epidemiology
Core-genome SNP clustering, transmission inference, and outbreak reconstruction for surveillance and public-health research.
Phylogenetics & phylodynamics
Maximum-likelihood and time-scaled trees, recombination handling, and molecular-clock and phylodynamic analysis.
Viral genomics & lineages
Consensus-genome assembly, variant calling, and lineage and clade assignment for viral surveillance and research.
Metagenomic pathogen detection
Taxonomic profiling and pathogen identification from metagenomic reads, including culture-independent detection.
Plasmids & mobile elements
Plasmid reconstruction and mobile-genetic-element detection to track horizontal transfer of resistance and virulence.
Virulence & comparative genomics
Virulence-factor detection and pangenome and comparative analysis to characterise strains and gene content.
The Pipeline
A representative pathogen-genomics workflow
A transparent, pathogen-aware sequence from raw reads to interpreted surveillance—each step suited to the organism and documented for reproducibility.
Adapted to your study: bacterial vs. viral, isolate vs. metagenomic, single genome vs. outbreak panel. We confirm the plan with you before any compute begins.
Intake & QC
Raw reads or assemblies are quality-checked—read quality, contamination, coverage, and species confirmation.
Tools: fastp · Kraken2 · CheckM
Assembly / consensus & typing
Genomes are assembled or consensus called, then typed by MLST, cgMLST, or serotype for standard nomenclature.
Tools: SPAdes · iVar · MLST
AMR, virulence & MGEs
Resistance genes, virulence factors, plasmids, and mobile elements are detected against curated databases.
Tools: AMRFinderPlus · abricate · mob-suite
Variant calling & alignment
Core-genome SNPs are called against a reference and a recombination-aware alignment is built for the panel.
Tools: snippy · snp-sites · Gubbins
Phylogenetics & clustering
Maximum-likelihood trees and SNP-distance clustering resolve relationships and candidate transmission clusters.
Tools: IQ-TREE · FastTree · SNP clusters
Phylodynamics & epidemiology
Time-scaled trees, molecular-clock, and lineage assignment place isolates in an epidemiological and surveillance context.
Tools: TreeTime · Nextstrain · Pangolin
Integration & reporting
Results become annotated trees, resistance and typing tables, cluster maps, and reproducible methods with every tool version.
Tools: ggtree · Microreact · versioned manifest
Tools & Technologies
Established, peer-reviewed tools—matched to your data
We select from the field's standard toolkit rather than forcing every dataset through one pipeline. A representative set of what we work with:
Assembly & QC
SPAdes
Unicycler
Flye
QUAST
CheckM
Typing
MLST
chewBBACA
SISTR
Kleborate
AMR & virulence
ResFinder
AMRFinderPlus
CARD / RGI
abricate
VFDB
SNP & alignment
snippy
snp-sites
Gubbins
minimap2
Phylogenetics
IQ-TREE
RAxML
FastTree
ggtree
Phylodynamics
BEAST2
TreeTime
Nextstrain
TransPhylo
Viral genomics
iVar
Pangolin
Nextclade
seqkit
Metagenomics & databases
Kraken2
MetaPhlAn
PubMLST
BV-BRC
Key Databases
The pathogen-genomics resources we draw on
Pathogen analysis is powered by curated reference genomes, typing schemes, and resistance databases. We build on the community's authoritative, versioned resources.
- NCBI RefSeq
- Reference genomes and annotation across microbial species.
- ENA
- The European Nucleotide Archive of raw reads and assemblies.
- GISAID
- Shared viral genome sequences for global surveillance.
- PubMLST
- Curated multi-locus and cgMLST typing schemes.
- CARD
- Comprehensive Antibiotic Resistance Database and ontology.
- ResFinder
- Acquired resistance genes and point mutations.
- VFDB
- Reference database of bacterial virulence factors.
- Nextstrain
- Real-time phylodynamic tracking and visualization.
- BV-BRC
- Bacterial and Viral Bioinformatics Resource Center.
Choosing an Approach
Isolate WGS vs. metagenomic vs. amplicon
Different sequencing strategies answer different pathogen questions. A quick orientation; we will help you match it to your study.
| Dimension | Isolate WGS | Metagenomic | Amplicon / targeted |
|---|---|---|---|
| Input | Cultured isolate | Whole sample | Targeted region / gene |
| Resolution | Strain-level, whole genome | Community & pathogen ID | Marker or region only |
| AMR & typing | Full profile | Partial, coverage-dependent | Targeted markers only |
| Culture needed | Yes | No (culture-independent) | No |
| Best suited to | Outbreaks & AMR surveillance | Unknown or unculturable | Fast, focused screening |
What You Receive
A complete, documented deliverable
Not just an assembly dropped in a folder—a surveillance-ready picture of each isolate and how they relate, documented so it reproduces.
- Quality-checked assemblies with species & typing calls (MLST/cgMLST)
- Antimicrobial-resistance & virulence gene profiles
- Plasmid & mobile-element findings, where applicable
- Core-genome SNP alignment & distance matrix
- Annotated phylogenetic tree & transmission clusters
- Viral consensus genomes & lineage calls, where applicable
- Reproducible methods with every tool & database version
Built for reproducibility, not just a result
Pathogen analysis follows documented best practices—species confirmation and contamination checks, recombination-aware alignment, curated and versioned resistance and typing databases, and phylogenies with support values—so a transmission cluster or a resistance call is real signal, not a database artifact or a mis-assembly. This is research, public-health, and surveillance work that your team interprets; genotype-based resistance results are not a clinical antimicrobial-susceptibility test, and clinical diagnosis and reporting remain with accredited laboratories and qualified professionals.
The practical payoff: your methods section writes itself, a reviewer can re-run the analysis, and a result from today can be reproduced a year from now. We will also tell you honestly when a design or sample size won't support the conclusion you're after.
FAQ
Microbiology & infectious disease questions
What microbiology, public-health, and infectious-disease teams most often ask before starting.
Bacterial and viral whole-genome sequencing (short- and long-read), metagenomic and amplicon data, and consensus genomes or assemblies — starting from raw reads, assemblies, or sequences from your core or public repositories like NCBI, ENA, and GISAID.
Yes. We detect resistance genes and mutations from genomes against curated databases like CARD and ResFinder. This is genotype-based research and surveillance — it is not a clinical antimicrobial-susceptibility test, which stays with an accredited laboratory.
Yes. We build core-genome SNP alignments, cluster isolates, reconstruct phylogenies, and estimate transmission relationships for genomic-epidemiology and surveillance research.
Yes. We generate consensus genomes, call variants, and assign lineages and clades (for example with Pangolin and Nextclade) for viral surveillance and research.
No. We provide research, public-health, and surveillance bioinformatics that your team interprets. We are not a clinical diagnostic laboratory; results are not a clinical diagnosis or a susceptibility report, and clinical decisions stay with accredited labs and qualified professionals.
Infectious disease is a research area we support through our core services — chiefly Genomics & Variant Analysis, Metagenomics & Microbiome, and Custom Pipelines & Software — applied to pathogen data. This page shows how they come together.
Related
Services that power infectious-disease work
Have pathogen data to track?
Tell us your organism, data type, and question—we'll scope it honestly, including if a different design would serve you better.