Estimating time and costs to get started with Nanopore
Integrating Nanopore sequencing into a classroom or teaching laboratory offers many benefits. However, estimating the time and total costs required to get started is essential for successful planning and implementation. This section provides some tips and observations to help educators understand the resources and time needed to bring Nanopore sequencing to their students.
When estimating costs, educators should consider both initial and recurring expenses. These include purchasing essential equipment, consumables, reagents, and sequencing kits, as well as ensuring access to appropriate computational resources. Time estimates should account for equipment setup, instructor preparation, and the time required to guide students through laboratory protocols and bioinformatics analyses.
It’s important to note that these are general guidelines, and several factors can influence both the time and cost of implementation. For example:
- Class size and the number of sequencing projects planned may affect the quantity of consumables and reagents required.
- Availability of existing laboratory equipment and computational resources can significantly reduce start-up costs.
- Instructor experience with molecular biology techniques and bioinformatics may influence preparation time and the level of support needed.
- Institutional purchasing agreements or discounts may reduce the costs of equipment and reagents.
Example prep and teaching activities and timings
| Activities | Estimated Duration | Items/Activities to Add Up Costs($) | Notes |
|---|---|---|---|
| Background research on Nanopore sequencing | (1–2) days | Training workshops (free-$ for travel or tuition) | Time for familiarization; consider workshops or online resources |
| Curriculum planning | (1–2) weeks | Lesson plans, assessments, teaching materials | Aligns activities with course objectives; includes material development |
| Protocol testing | (1) month | Reagents ($$$), consumables ($$), staff time | Trial runs with aides or TAs; optimize protocols for classroom |
| Sample collection | (1) 2-hour lab section | Collection supplies ($), travel ($) and equipment ($$) | Depends on sample type (e.g., environmental, lab specimens) |
| DNA extraction | (1–2) 2-hour lab sections | Reagents ($$), consumables ($), equipment ($$$) | Includes DNA isolation and quality checks; depends on sample type |
| Library preparation | (1-2) 2-hour lab section | Sequencing kits ($$), consumables ($), reagents ($$) | Laboratory staff or instructor pools samples and generates libraries |
| DNA sequencing | (1) 2-hour lab section | Flow cells ($-$$), sequencing kits ($$), compute resources | Some samples may require 1-hour runs; others may need 24+ hours |
| Data analysis | (2) 2-hour lab sections | Software subscriptions ($), cloud resources (free-$) | Includes bioinformatics tools and interpretation; longer steps like basecalling occur outside class time |
| Evaluation and feedback | (1) week | Instructor time, survey tools, debriefing materials | Grading assessments, collecting feedback, and debriefing instructional staff |
Example costs - Nanopore equipment
This table outlines the estimated minimal startup costs for purchasing your first set of Nanopore sequencing materials, assuming that you already have most basic molecular biology reagents and equipment. The potential education discounts are included for illustrative purposes only—contact Oxford Nanopore to inquire on available education discounts.
| Item | Section/Class Quantity | Base Cost | Total at Base Cost | Education Discount Price* | Total w/Discount |
|---|---|---|---|---|---|
| MinION Startup Pack (MinION flow cell Flongle flow cells, sequencing kit) | 1 | $2,000 | $2,000 | $1,600 | $1,600 |
| Flongle and adapter | 1 | $1,460 | $1,460 | 0 (included in startup pack) | |
| Magnetic rack | 6 | $59 | $354 | $59 | $354 |
| MacBook computer | 1 | $2,800 | $2,800 | $2,400 | $2,400 |
| Total Startup Costs | $6,614 | $4,354 |
*The provided educational discounts are illustrative and may vary depending on institutional agreements or vendor promotions
Example costs - Nanopore reagents and consumables
This table provides an overview of the estimated costs for different Nanopore sequencing kit types and associated reagents when used in classroom settings. It includes base costs, costs per sample or reaction, and potential educational discounts. The table highlights the potential costs for a class of 24 students, assuming standard consumables and reagents.
16S Kit (6 x 24 samples) - Microbial diversity
| Nanopore Sequencing Kit Type | Base Cost | Total per Sample/Run | Education Discount Price* | Total per Sample/Run w/Discount |
|---|---|---|---|---|
| Nanopore 16S Kit | $900.00 | $6.25 | $400.00 | $2.78 |
| Norgen DNA extraction kit and swabs (50 preps) | $638.00 | $12.76 | $638.00 | $12.76 |
| NEB LongAmp Taq (100 rxn) | $161.00 | $1.61 | $128.00 | $1.28 |
| Flongle (12 pack - 1 Flongle per run) | $67.00 | $2.79 | $67.00 | $2.79 |
| Consumables ($4 per student) | $96.00 | $4.00 | $96.00 | $4.00 |
| Potential cost per student/run | $27.41 | $23.61 | ||
| Total for class of 24 | $657.88 | $566.63 |
Rapid Barcoding Kit (6 x 24 samples) - DNA barcoding and small genomes
| Nanopore Sequencing Kit Type | Base Cost | Total per Sample/Run | Education Discount Price* | Total per Sample/Run w/Discount |
|---|---|---|---|---|
| Nanopore Rapid Barcoding Kit | $699.00 | $4.85 | $110.00 | $0.76 |
| Low-cost "homemade" DNA extraction (24 preps) | $24.00 | $1.00 | $24.00 | $1.00 |
| Low-cost Taq and PCR reagents (24 preps) | $50.00 | $2.08 | $50.00 | $2.08 |
| Flongle (12 pack - 1 Flongle per run) | $67.00 | $2.79 | $67.00 | $2.79 |
| Consumables ($4 per student) | $96.00 | $4.00 | $96.00 | $4.00 |
| Potential cost per student/run | $14.73 | $10.64 | ||
| Total for class of 24 | $353.50 | $255.33 |
Ligation Kit (6 samples) - Small genomes
| Nanopore Sequencing Kit Type | Base Cost | Total per Sample/Run | Education Discount Price* | Total per Sample/Run w/Discount |
|---|---|---|---|---|
| Nanopore Ligation Kit | $699.00 | $233.00 | $110.00 | $36.67 |
| DNA extraction kit (example, NEB Monarch) 50 samples; 6 runs | $517.00 | $20.68 | $413.60 | $16.54 |
| NEB companion module (24 reactions); 6 runs | $1,025.00 | $85.42 | $820.00 | $68.33 |
| MinION flow cell (1 per run - assuming 2 runs, washed and reused) | $750.00 | $375.00 | $450.00 | $225.00 |
| Consumables ($4 per student) | $96.00 | $4.00 | $96.00 | $4.00 |
| Potential cost per student/run (2 runs or non-barcoded samples, 24 students) | $718.10 | $350.54 | ||
| Total for class of 24 | $718.10 | $350.54 |
*The provided educational discounts are illustrative and may vary depending on institutional agreements or vendor promotions
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