The MinION looks cheap next to other sequencers, and you can have reads within hours. That makes "should we just buy one?" a common lab-meeting question. The honest answer depends less on the device and more on how often you'll use it, and who in the lab will run it.
01What a run really costs
| Item | What to know |
|---|---|
| Flow cell | About $800 for a single flow cell on the Oxford Nanopore store at the time of writing, less per flow cell in multi-packs. Some can be washed and reused for later runs, with lower output. |
| Library prep kit | Bought separately, usually enough for several libraries. Barcoding kits let you pool samples on one flow cell. |
| Lab reagents | Beads, enzymes from other suppliers, tubes and QC assays add up per run. |
| Computer | The most accurate basecalling needs a capable GPU. Without one, basecalling is slow, or you use faster, less accurate models. |
| Your time | Library prep, loading, monitoring the run and analysis. The first few runs take longest. |
02Cost per sample: why barcoding matters
A flow cell costs the same whether it carries one sample or twenty. With barcoding, several samples share one run, so the cost per sample drops quickly. This works well for small genomes, such as bacterial isolates or plasmids, where each sample needs only a small share of the run's output. For a large genome at high coverage, one sample may need a whole flow cell or more.
03The costs people forget
- The learning curve. Early runs often give less output, because library prep and loading take practice. Budget at least one practice run.
- Flow cell shelf life. Flow cells have an expiry and need a pore check before use. Buying many at once only helps if you'll use them in time.
- Storage and backup. Raw signal files are large. Plan disk space before the first run.
- Who runs it. If only one person knows the workflow, the device sits idle when they leave.
04When in-house makes sense
| In-house MinION tends to win when... | Sending samples out tends to win when... |
|---|---|
| You'll run regularly (for example, every month) | It's a one-off project |
| Speed matters, for example outbreak or pathogen work | You need very high accuracy at large scale |
| Your samples are small genomes you can barcode together | You have many large genomes at high coverage |
| Someone in the lab can own the workflow | Nobody has time to learn and maintain it |
Many labs do both: they run small, fast jobs in-house and send big projects to a core or company.
Check your DNA before any run
Enter your concentration, purity and integrity and see what needs fixing, in-house or outsourced. No signup.
Common questions
Is nanopore accurate enough now?
Accuracy has improved a lot with newer chemistry and basecalling models. Whether it's enough depends on your question, so check recent papers in your field that used the same chemistry.
Can I reuse a flow cell?
Some flow cells can be washed and reloaded for another run, usually with lower output. It works best when the next samples use different barcodes.
Do I need a powerful computer?
For the most accurate basecalling, a capable GPU helps a lot. Some groups basecall on a shared university cluster instead.
The First Nanopore Run Kit
Your first MinION run, without wasting a flow cell: check your DNA, protect the flow cell warranty, read the MinKNOW screen, rescue a bad run and record every version. 24-page guide + run workbook.
$29 one-time · 14-day money-back guarantee · instant download