design_primers
Design a forward + reverse primer pair to amplify the subject (pydna primer_design), with Tm, Ta and suggested Taq/Phusion cycling programs. Emits both primers so a downstream pcr_amplify runs on them — the design→PCR→gel loop.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | minimum primer length (pydna `limit`). In bp. Advanced. | |
| _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. | |
| _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. | |
| target_tm | No | target melting temperature (pydna default 55). In °C. | |
| conditions | No | salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the target Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to the nearest-neighbour defaults when there are none. Advanced. | |
| forward_primer | No | supply one primer to design only its mate. Advanced. | |
| reverse_primer | No | supply one primer to design only its mate. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| ta | Yes | suggested annealing temperature [°C] | |
| forward | Yes | forward primer 5'→3' (wire into pcr_amplify) | |
| program | Yes | suggested Taq cycling program | |
| reverse | Yes | reverse primer 5'→3' (wire into pcr_amplify) | |
| forwardTm | Yes | forward primer Tm [°C] | |
| productTm | Yes | amplicon melting temperature [°C] (Rychlik 1990, at the run's own monovalent salt) — 70% of `ta` on the Taq path | |
| reverseTm | Yes | reverse primer Tm [°C] | |
| productLen | Yes | amplicon length [bp] |