Key takeaways
- The biggest cost driver is how many bases need to be sequenced: genome size × coverage × number of samples.
- A human genome at 30× needs roughly 100 Gb of sequence; a bacterial genome at 100× needs well under 1 Gb, so many bacterial samples can share one run.
- Long-read and hybrid sequencing cost more per sample, but they answer questions short reads can't.
- Library prep, sample extraction and bioinformatics are separate lines. Check whether you need each one.
- Larger batches usually lower the price per sample.
1. Genome size and coverage set the number of bases to be sequenced
Sequencing is priced mainly by the number of bases a lab has to sequence. For whole genome sequencing (WGS), that number is simple to estimate:
Raw bases to sequence ≈ genome size × target coverage
Coverage (or depth, written as 30×, 50× and so on) is how many times, on average, each base of the genome is read. Higher coverage gives more confident variant calls but means more bases to pay for.
| Organism | Genome size | Typical coverage | Bases to sequence per sample |
|---|---|---|---|
| Human | ~3.1 Gb | 30× | ~95–100 Gb |
| Mouse | ~2.7 Gb | 30× | ~80 Gb |
| Zebrafish | ~1.4 Gb | 30× | ~42 Gb |
| Arabidopsis thaliana | ~135 Mb | 30–50× | ~4–7 Gb |
| Yeast (S. cerevisiae) | ~12 Mb | 50–100× | ~0.6–1.2 Gb |
| E. coli | ~4.6 Mb | 100× | ~0.5 Gb |
This is why a single human genome costs far more than a bacterial one: it needs around 200 times more sequencing. It is also why bacterial and yeast genomes are usually pooled, with many samples sharing one sequencing run.
How much coverage do you really need?
- ~30× for germline variant calling in human and other diploid genomes. This is the most common choice.
- 60–100× for tumour samples or mosaic variants, where a variant may be present in only a fraction of cells.
- 50–100× for de novo assembly of small genomes with short reads.
- Lower coverage can be enough for population genetics, ancestry or copy-number screening.
Asking for more coverage than your analysis needs is the most common way to overspend. If you are unsure, email or call our scientists before you order.
2. Sequencing technology
The platform you choose changes both the price per gigabase and what you get out of the data.
| Technology | Best for | Cost per sample |
|---|---|---|
| Short-read (Illumina, Ultima Genomics) | SNVs and small indels, population studies, most resequencing projects | Lowest |
| Long-read: PacBio HiFi | Highly accurate long reads: structural variants, repeats, phasing, high-quality assemblies | Higher |
| Long-read: Oxford Nanopore | Very long reads, structural variants, native methylation, assemblies | Higher |
| Hybrid (Nanopore + Illumina) | Complete, polished assemblies of bacterial and other small genomes | Moderate, often with assembly included |
For a standard human resequencing project, short reads are usually the most cost-effective choice. When the biology lives in repeats, rearrangements or haplotypes, long reads are worth the extra cost.
3. Library preparation
Library prep turns your DNA into something the sequencer can read, and it is priced separately from sequencing.
- PCR-free libraries give the most even coverage and fewer artefacts, but need more input DNA.
- Standard (PCR-based) libraries work with less input DNA.
- Low-input and FFPE libraries rescue limited or degraded samples, at a higher price per sample.
- If you send ready-made libraries, you only pay for sequencing (see sequencing only).
Price differences between library types depend mostly on each lab's protocol and how automated it is, so compare them per provider rather than assuming one type is always cheaper.
4. Sample type and extraction
Sending purified genomic DNA is the simplest and cheapest option. If the lab has to extract DNA from blood, tissue, cells, plants, fungi or bacteria, extraction and QC are added to the price. FFPE tissue usually costs the most to process because the DNA is fragmented and chemically damaged.
5. Bioinformatics
The standard deliverable is raw data (FASTQ files). Many projects also need analysis: alignment to a reference, variant calling and annotation, or de novo assembly and gene annotation for new genomes. Analysis is a separate line in your estimate, so you can choose raw data only if your group already has a pipeline. See our bioinformatics services.
6. Number of samples
Labs sequence on fixed-size flow cells. A large batch fills them efficiently, so the price per sample usually drops as the project grows. If you expect more samples later, mention it when you request a quote, because it can change the best way to plan the runs.
A worked example
Suppose you want 12 human samples from blood, 30× coverage, short reads, with variant calling:
- Data: 3.1 Gb × 30 ≈ 95 Gb per sample, about 1.1 Tb in total.
- Extraction from whole blood, plus a PCR-free library for each sample.
- Short-read sequencing on a high-output instrument.
- Alignment, variant calling and annotation for 12 samples.
Each of these is a line in your estimate. Change any one (for example 50× instead of 30× coverage, or raw data only) and the total changes accordingly. Send your project details through the WGS quote request and our team will reply with an estimate as soon as possible.
Frequently asked questions
What coverage do I need for human whole genome sequencing?
30× is the standard for germline variant calling in human samples. Tumour samples are usually sequenced deeper (often 60–100×) to detect variants present in only part of the cells, while population studies and screening projects sometimes use lower coverage.
Is whole exome sequencing cheaper than whole genome sequencing?
Usually yes per sample, because only the protein-coding part of the genome (about 1–2%) is sequenced. Exome sequencing misses non-coding regions and is less even in coverage, so the right choice depends on your question. See our WES estimate to compare.
Why does long-read sequencing cost more than short-read sequencing?
Mainly because each long-read run produces far fewer bases, while the flow cells or SMRT Cells and reagents cost about as much or more. Spreading a higher run cost over fewer gigabases makes every gigabase more expensive. Library prep also adds cost: long reads need high-molecular-weight DNA, gentle handling and size selection, which take more input DNA and more hands-on work. You pay more, but you resolve repeats, structural variants and phasing that short reads cannot.
Does the price include data analysis?
Not by default. Raw FASTQ files are the standard deliverable; alignment, variant calling, assembly or annotation can be added as bioinformatics analysis and appear as a separate line in your estimate.
Are the prices on QuickSeq final?
No. Any price we give before the formal quote is an estimate based on your project details. Our team reviews every request and sends a formal quote as soon as possible, with the binding price and terms.
