Single-Virus Genome Sequencing Services

Pilot Particle Recovery before Scaling the Project

A single-virus project begins with sample and particle QC. The pilot evaluates concentration, background, sorting discrimination and amplification success before hundreds of reactions are committed.

A pilot tests viral enrichment, particle isolation, amplification and sequencing before project expansion.

Illumina paired-end sequencing is the primary route for many amplified DNA reactions because it supports scalable per-particle libraries and robust base accuracy. Long reads may be considered when amplified DNA yield and genome structure support them, but amplification bias and chimeras must be evaluated. RNA viruses are not included in the default scope and require a separately designed reverse-transcription workflow.

Short-read depth is assigned per successful amplification rather than uniformly across all sorted particles. Reactions with weak yield, high background or abnormal amplification profiles may be screened before full library production. This staged approach directs sequencing effort toward interpretable genome candidates while preserving failed and excluded reactions in the project QC record.

Matched bulk viromics can add population context. Single-particle genomes provide discrete genome structures and microdiversity, while bulk reads estimate how broadly those genomes occur in the sampled community. Combining the two routes is optional, but it often helps distinguish a rare recovered genome from a widely represented population that simply assembled poorly.

Build and Qualify One Genome Candidate at a Time

Each amplified reaction is processed as an independent genome candidate. Background, co-isolation and amplification artifacts are evaluated before genomes are compared.

Read and amplification quality control

Adapters and low-quality bases are removed, and library yield and complexity are reviewed per particle. Reads detected in negative controls or matching common host and reagent backgrounds are flagged.

Coverage uniformity is inspected because whole-genome amplification can create strong local peaks and missing regions. Duplicate or near-identical reactions are compared to detect recurrent contamination and genuine population structure.

De novo assembly and viral identification

Reads are assembled independently for each reaction. Viral sequence detection combines hallmark genes, genome organization and similarity evidence rather than relying on one database match.

Contigs are grouped cautiously when a reaction produces multiple components. Circularity, terminal repeats and coverage patterns are assessed where the data support them. A draft designation is retained when closure is not demonstrated.

Genome quality, annotation and comparison

Genome completeness and contamination are assessed with current viral reference frameworks, while host-like or bacterial carryover is reported. Open reading frames, protein families and selected functional categories are annotated for quality-eligible genomes.

Genome clustering, average nucleotide identity, shared-gene analysis and variant comparison reveal species groups and within-population diversity. Putative host prediction can be added from sequence evidence, but it remains probabilistic unless experimentally validated.

Amplification artifacts require explicit review. Uneven coverage, chimeric joins, recurrent sequences in controls and conflicting taxonomic signals can reduce confidence in an assembly even when its length appears substantial. Quality ranking therefore considers multiple lines of evidence and retains partial genomes when they are informative, rather than forcing every reaction into a complete-genome category.

Annotation is prioritized for genomes that pass agreed quality thresholds. Hallmark genes, structural proteins, replication functions and selected auxiliary genes can be compared across clusters, while hypothetical proteins remain labeled as such. The result supports genome discovery and candidate selection without converting sequence prediction into proof of infectivity or biological function.

Per-particle quality control, de novo assembly and viral genome ranking produce a curated genome catalog.

Understand the Result View

A result view separates high-quality single-virus genomes from partial, contaminated and unresolved reactions.

Recover Viral Diversity Beyond Bulk Assembly

Single-virus genomics is most informative when the scientific value of individual genomes justifies the additional isolation and amplification effort. Bulk viromics remains the more efficient first choice for community composition and relative abundance.

Recovered genome candidates can also serve as references for later host-linkage analysis. CRISPR spacer matches, sequence-composition evidence, proximity-based measurements or isolate experiments may be compared with the genome catalog in a separate project. Each evidence source has different resolution and error modes, so a predicted host is kept distinct from an experimentally confirmed host. This separation lets customers extend the project without overstating what single-particle genome sequencing establishes on its own.

Single-virus genomics supports rare-virus discovery, microdiversity analysis and reference-genome expansion.

Choose Single-Virus Genomics When Individual Genomes Matter

Best suited to: DNA-virus-rich fractions where rare genomes, strain separation or particle-level microdiversity are central and a pilot can evaluate sorting and amplification feasibility.

When another approach is more suitable: use ordinary viral whole-genome sequencing for a pure isolate and viromics for broad community profiling. Infectivity, host range, viral activity and RNA-virus analysis require separate workflows.

Provide sample matrix and volume, particle concentration or proxy, enrichment and nuclease-treatment steps, storage, expected DNA or RNA genome type, target marker if any, desired number of particle reactions and whether matched viromics is available.