plan_thermocycler_program
Read-only
Plan the cycling programme for an amplicon on a NAMED enzyme, and check the reaction against that manufacturer's own published limits. The extension rate and the denaturation step come from the product's datasheet and protocol manual; the annealing temperature is yours (from design_primers or pcr_amplify), and anything the manufacturer does not publish comes from the pydna-faithful Taq or Phusion/Q5 preset — the result says which numbers came from where. The check reports the product as a percentage of the vendor's stated maximum, the extension time its rate implies, the substitutions expected per molecule and the fraction of molecules that should be error-free, each finding quoting the specification line it rests on.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| steps | No | 3-step keeps a separate annealing stage; 2-step merges it into the extension, which is what a high-Tm pair allows. `auto` lets the builder decide from the primer Tms. Advanced. | auto |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| cycles | No | cycles in the main block. | |
| enzyme | No | the cataloged product to plan on, or `generic` for the preset alone. Its datasheet supplies the extension rate and, where its manual states one, the denaturation step. Values: generic (Generic preset (no datasheet)), takara-taq (Takara Bio · TaKaRa Taq / EmeraldAmp GT), takara-ex-taq (Takara Bio · TaKaRa Ex Taq / EmeraldAmp MAX), takara-la-taq (Takara Bio · TaKaRa LA Taq), takara-ex-premier (Takara Bio · TaKaRa Ex Premier), primestar-gxl (Takara Bio · PrimeSTAR GXL DNA Polymerase), primestar-hs (Takara Bio · PrimeSTAR HS DNA Polymerase), primestar-max (Takara Bio · PrimeSTAR Max DNA Polymerase Ver.2), primestar-longseq (Takara Bio · PrimeSTAR LongSeq DNA Polymerase), cloneamp-hifi (Takara Bio · CloneAmp HiFi PCR Premix), speedstar-hs (Takara Bio · SpeedSTAR HS DNA Polymerase), terra-direct (Takara Bio · Terra PCR Direct Polymerase Mix), titanium-taq (Takara Bio · Titanium Taq DNA Polymerase), advantage-hd (Takara Bio · Advantage HD Polymerase Mix), qiagen-taq (QIAGEN · Taq DNA Polymerase), qiagen-hotstartaq (QIAGEN · HotStarTaq DNA Polymerase). | generic |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| anneal_c | Yes | annealing temperature [°C] for the pair — the Ta the Tm model gave you, not a guess this tool makes. In °C. | |
| touchdown | No | start with a touchdown block: the annealing temperature starts high and drops each cycle to the Ta, so early cycles favor the specific product (Korbie & Mattick 2008). | |
| gc_percent | Yes | product GC [%], which decides whether the vendor's GC window is cleared. In %. | |
| polymerase | No | which annealing convention and which preset supplies whatever the datasheet does not. Values: taq (Taq), dbd (Phusion / Q5 (DNA-binding domain)). | taq |
| amplicon_bp | Yes | product length [bp] — pcr_amplify and design_primers both emit it. | |
| touchdown_cycles | No | touchdown cycles before the main block (they add to `totalCycles`). Only applies when touchdown is true. | |
| touchdown_delta_c | No | how far the annealing temperature drops per touchdown cycle. In °C. Only applies when touchdown is true. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| program | Yes | the planned programme as a thermocycler would take it, stage by stage | |
| findings | Yes | the reaction check: each finding with its severity, its sentence and the vendor line it quotes. Empty for a reaction inside every published limit, and absent entirely for `generic`, which has no limits to check. | |
| denatureC | Yes | per-cycle denaturation temperature [°C] actually planned | |
| denatureSec | Yes | per-cycle denaturation time [s] actually planned | |
| totalCycles | Yes | cycles including any touchdown block | |
| extensionSec | Yes | extension time [s] this amplicon needs at the enzyme's published rate | |
| fromDatasheet | Yes | which of the planned numbers came from the product (the rest are the preset’s) — the same list the panel turns into its sentence |