Non-model organisms sequencing & viral genome analysis

De Novo Genome Assembly for Species Without a Reference

When no reference genome exists, SeqMatic builds one from scratch through de novo assembly: sequencing reads are generated and computationally assembled into contigs without aligning to a prior reference. This differs from resequencing (aligning reads to an existing reference) in both approach and timeline. De novo projects require more extensive bioinformatics work to assemble and annotate a new genome. SeqMatic’s bioinformatics team supports this end-to-end, from assembly through annotation.

DNA and microbial illustration

Applications of Non-Model Organism Sequencing

Application	What It Enables
Population genetics research	Understanding genetic variation within and between populations
Reference genome generation (De Novo)	Building a first-ever genomic reference for a species
Agricultural breeding programs	Trait selection and genetic improvement in crops and livestock
Genome-wide association studies (GWAS)	Linking genetic variants to traits or disease
Comparative genomic studies	Cross-species evolutionary and functional comparisons
Conservation & wildlife genomics	Genetic diversity assessment and endangered species management

Examples of Organisms Sequenced at the SeqMatic Laboratory

Category	Examples of Non-Model Organisms
NHP	Monkey, apes
Crops & plants	Soybeans, cotton, wheat, grape, tomato, potato
Marine life	Salmon, catfish
Livestock	Cattle, pig, horse, chicken
Wildlife	Dog, rat, squirrel, banana slugs

Sample Types We Accept

Sample Category	Examples
Whole specimen / tissue biopsy	Animal, plant, insect, and marine tissue
Non-invasive wildlife sampling	Hair, feathers, fecal, shed skin, museum and voucher specimens
Environmental samples	Soil, water, and other environmental material for biodiversity and eDNA studies

For exact input amounts and purity thresholds by platform refer to existing Sample Input Recommendations

Why SeqMatic for Non-Model Organism Sequencing

Sequencing a species with no existing reference genome takes different expertise than routine human or mouse sequencing, where reference, established QC benchmarks, and off-the-shelf pipelines already exist. SeqMatic brings the scientific expertise, flexible workflows, and rigorous quality practices needed to address these more complex sequencing projects.

De novo assembly & annotation, not just alignment: Most projects start with no reference genome. Our bioinformatics team builds one from scratch: genome assembly, repeat and gene structure prediction, and functional annotation.

Built for atypical, field-collected samples: Wildlife tissue, environmental swabs, plant material, museum specimens, and other non-standard inputs that don’t behave like clean human blood or cultured cell lines.
QC that doesn’t rely on a reference genome: Every extraction and library is validated independently (Qubit, TapeStation, qPCR, test sequencing) before a species-specific pipeline is built.
Platform strategy matched to genome complexity: Heterozygosity, repeat content, and ploidy vary widely across non-model species; we combine short-read, long-read, and hybrid assembly approaches (Illumina, PacBio REVIO, Oxford Nanopore) based on what a given genome requires.
Custom pipeline design per species: From soybean to banana slug, the workflow is built around the organism and research question rather than forced through one standard template.
Rigorous Quality Standards: Samples are processed under a CAP-accredited and CLIA-certified quality management system, ensuring high analytical rigor, traceability, and standardized SOP execution, while the specific assay and data output remain strictly designated for Research Use Only (RUO) and not for clinical diagnostic decision-making.

Sequencing Platforms

Libraries are sequenced across SeqMatic’s full platform lineup, matched to each project’s read length and depth requirements: Illumina or Ultima Genomics for short read sequencing, and PacBio or Oxford Nanopore for long read sequencing.

SeqMatic’s team helps determine the right platform for each project during consultation, based on the read length, depth, and accuracy the research question requires.

Application	Library Type	Recommended Depth
Genome survey (size, heterozygosity, repeat estimation)	WGS (survey/low-pass)	≥50x
De novo assembly (short read)	De Novo WGS (short-read)	100x or more
De novo assembly (long-read / hybrid)	De Novo WGS (long-read/hybrid)	[confirm]
Population genetics / GWAS resequencing	WGS	[confirm]

Frequently Asked Questions

Can SeqMatic build a reference genome for a species that's never been sequenced before?

Yes. Generating a first-ever reference genome is a core part of this service, not a special request. Project scope and timeline are typically confirmed during initial consultation once the target species and available sample material are known.

What if I only have raw tissue or field-collected specimens; not extracted DNA/RNA?

That’s fine. SeqMatic’s Extraction Services handle nucleic acid extraction from the sample itself, so raw tissue or whole specimens can be submitted directly rather than requiring pre-extracted material.

I'm not sure which platform or sequencing depth my species needs. Can SeqMatic help me plan it?

Yes, through Project Planning & Consultation, where sequencing strategy includes platform choice, coverage depth, short-read vs. long-read vs. hybrid is designed around your specific species and research goals before the project starts.

How do I ship or submit wildlife tissue or other unusual sample types?

Sample-specific handling and shipping guidance is covered in SeqMatic’s Sample Submission Instructions. Check there before shipping field-collected or wildlife material.

What happens if my samples don't pass initial quality control?

QC reports are reviewed with you to decide which samples qualify for library preparation as submitted, and which need alternative library prep or resubmission. Nothing proceeds to sequencing without that review.

Why does de novo sequencing cost more than resequencing?

De novo sequencing has no reference to align against, so it requires deeper coverage, often a combination of short-read and long-read data, and substantially more bioinformatics work to assemble and annotate a genome from scratch. Resequencing skips the assembly step and compares reads directly to an existing reference.

Should I use short-read, long-read, or both for my project?

Short-read sequencing is cost-effective and highly accurate per base but produces more fragmented assemblies, especially in repeat-rich genomes. Long-read platforms (PacBio REVIO, Oxford Nanopore) produce longer, more contiguous assemblies and are generally preferred for de novo work, often combined with short reads in a hybrid approach for the most complete result.

Does SeqMatic provide bioinformatics analysis for non-model organisms?

Yes. SeqMatic provides custom bioinformatics at three tiers: Primary (alignment and quantification), Secondary (QC, normalization, and differential expression), and Tertiary (pathway, gene ontology, and functional interpretation) and can go deeper per customer request.

How is my sequencing data stored and delivered once a project is complete?

See Sample and Data Storage and Data Transfer Options for storage duration and secure delivery options.