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Total cost of ownership"Free" hides the work spcfy takes over.
A license-free pipeline isn't zero-cost. Someone builds it, runs it, babysits it, pays for the compute, then turns the OTU table into figures and queries it against the actual question. spcfy has no RAM to size, no wall-clock to watch, and folds visualization and querying into the platform.
Hidden effort behind each solution
Build, run, staff and compute time not covered by the direct fee. Bar length is the effort level, not a precise measurement.
The same comparison as a table
| Solution | Pricing model | Cost profile | + hidden: build · run · staff · compute |
|---|---|---|---|
| spcfy | subscription tier plus a per-sample fee, current rates on /pricing | €€ | low, hosted, visualization & querying built in |
| UseGalaxy.eu | free public access | free | medium, tool choices, manual QC, shared-quota waits |
| QIIME2 / DADA2 | free / open source | free | high, install & maintain, own HPC/RAM, staff time |
| nf-core/ampliseq | free / open source | free | high, setup + orchestration, HPC/cloud, admin |
| Apscale | free / open source | free | medium, own hardware/cloud, BYO storage, maintenance |
| Seqera Platform | consumption (CPU-h, storage) | €€ | medium, metered compute + pipeline upkeep |
| PEMA / MetaWorks | free / open source | free | high, install, own DBs, HPC/cloud, staff time |
| Managed service | individual quote, per sample/run | €€€ | low, provider does the work |
| LLM API | token / usage | €€€ | high, non-reproducible, data leaves your control |
On spcfy's pricing: a subscription tier plus a per-sample charge, not one or the other, the per-sample rate drops at higher volume. See /pricing for current numbers, this page compares structure and effort, not a specific quote. spcfy also gives you a shared repository: a group can share its SPIN-linked results instead of each member rebuilding them.
Budgeting the hours for a 1,000-sample study
A one-off run, in a lab starting without an existing setup. The hours are a model, not measurements from a specific project, and your own numbers are the ones that count. Where staff time is effectively free (a funded student, existing HPC), the open-source column looks better outright; where it isn't, the two converge fast.
| Cost line | Open-source on own HPC | spcfy |
|---|---|---|
| Pipeline build / setup | ~40 h bioinformatician | 0 h |
| Run + babysitting / QC | ~20 h | analysis time only |
| Compute (CPU · RAM · storage) | cloud/HPC bill | included |
| Build visualizations / reports | ~10 h | in platform |
| Query results against the hypothesis | ~10 h analyst | interface / spcfAI |
| Direct fee | 0 € license | tier + per-sample, see /pricing |
Turning the ~80 hours into money depends on your own staff cost and the current spcfy rates on /pricing. spcfAI natural-language querying is in alpha and its free-token allowance isn't decided yet, treat it as included analyst effort either way.
Compare: Overview · Feature Matrix · Cost · Benchmark · Alternatives