> ## Documentation Index
> Fetch the complete documentation index at: https://primerlab-genomic.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# Customization

# Customization Guide

Learn how to customize PrimerLab parameters for your specific research needs.

## Overview

PrimerLab's design can be customized at three levels:

1. **Presets** — Pre-configured parameter sets
2. **Config Files** — YAML-based configuration
3. **CLI Overrides** — Command-line parameter adjustments

***

## Customizable Parameters

### Primer Properties

| Parameter      | Config Path              |   Range  | Description                 |
| -------------- | ------------------------ | :------: | --------------------------- |
| **Length**     | `parameters.primer_size` | 15-40 bp | Primer length in base pairs |
| **Tm**         | `parameters.tm`          |  45-75°C | Melting temperature         |
| **GC Content** | `parameters.gc`          |  20-80%  | Guanine-Cytosine percentage |

```yaml theme={null}
parameters:
  primer_size:
    min: 18
    opt: 22
    max: 28
  tm:
    min: 58.0
    opt: 60.0
    max: 62.0
  gc:
    min: 40.0
    max: 60.0
```

### Amplicon Properties

| Parameter         | Config Path                           | Typical Values |
| ----------------- | ------------------------------------- | -------------- |
| **Product Size**  | `parameters.product_size_range`       | `[[100, 300]]` |
| **Max Poly-X**    | `parameters.max_poly_x`               | 3-5            |
| **Max Self-Comp** | `parameters.max_self_complementarity` | 4-8            |

```yaml theme={null}
parameters:
  product_size_range: [[150, 250]]
  max_poly_x: 4
  max_self_complementarity: 6
```

### QC Thresholds

| Parameter         | Config Path         |    Recommended    |
| ----------------- | ------------------- | :---------------: |
| **Hairpin ΔG**    | `qc.hairpin_dg_min` | -2 to -4 kcal/mol |
| **Dimer ΔG**      | `qc.dimer_dg_min`   | -5 to -8 kcal/mol |
| **Tm Difference** | `qc.tm_diff_max`    |       2-5°C       |

```yaml theme={null}
qc:
  mode: standard  # strict, standard, relaxed
  hairpin_dg_min: -3.0
  dimer_dg_min: -6.0
  tm_diff_max: 3.0
```

***

## Overriding Presets

Start with a preset and override specific values:

```yaml theme={null}
preset: diagnostic_pcr

# Your overrides
parameters:
  tm:
    opt: 62.0  # Higher than default 60°C
  product_size_range: [[100, 300]]  # Larger than default 80-200

qc:
  mode: standard  # Relax from default strict
```

***

## Application-Specific Recommendations

### 🧬 Clinical Diagnostics

```yaml theme={null}
preset: diagnostic_pcr

parameters:
  primer_size:
    opt: 22
  tm:
    min: 58.0
    opt: 60.0
    max: 62.0
  product_size_range: [[80, 150]]

qc:
  mode: strict
```

**Key Points**:

* Short amplicons (80-150 bp) for rapid cycling
* Strict QC to avoid false positives
* Tight Tm range for reproducibility

***

### 🔬 Gene Cloning

```yaml theme={null}
preset: cloning_pcr

parameters:
  primer_size:
    min: 28
    opt: 32
    max: 40
  tm:
    opt: 64.0
  product_size_range: [[500, 2500]]

cloning:
  add_restriction_overhang: true
  common_sites:
    - EcoRI
    - BamHI
```

**Key Points**:

* Longer primers to accommodate restriction sites
* Higher Tm for added 5' tails
* Configure restriction sites in `cloning` section

***

### 🌿 Environmental DNA (eDNA)

```yaml theme={null}
preset: dna_barcoding

parameters:
  tm:
    min: 48.0
    opt: 52.0
    max: 56.0
  gc:
    min: 30.0
    max: 70.0

qc:
  mode: relaxed
```

**Key Points**:

* Lower Tm for degraded templates
* Wide GC range for diverse taxa
* Relaxed QC for challenging samples

***

### 📊 qPCR / TaqMan

```yaml theme={null}
workflow: qpcr
mode: taqman

parameters:
  tm:
    opt: 60.0
  product_size_range: [[70, 150]]

probe:
  tm:
    min: 68.0
    opt: 70.0
    max: 72.0
  exclude_5_g: true
```

**Key Points**:

* Probe Tm should be \~10°C higher than primers
* Avoid G at 5' end of probe (quenches fluorophore)
* Small amplicons for efficient amplification

***

## Creating Custom Config Files

### Step 1: Start from Template

```bash theme={null}
# Generate a template config
primerlab init --workflow pcr --output my_config.yaml
```

### Step 2: Edit Parameters

Open `my_config.yaml` and modify as needed.

### Step 3: Validate

```bash theme={null}
primerlab validate my_config.yaml
```

### Step 4: Run

```bash theme={null}
primerlab run pcr --config my_config.yaml
```

***

## CLI Quick Overrides

Override without editing config:

```bash theme={null}
# Override Tm
primerlab run pcr --config base.yaml --tm-opt 62

# Override product size
primerlab run pcr --config base.yaml --product-min 100 --product-max 250

# Override QC mode
primerlab run pcr --config base.yaml --qc-mode relaxed
```

***

## See Also

* [Presets Reference](/docs/reference/presets)
* [Configuration Reference](/docs/reference/config)
* [Understanding Results](/docs/concepts/understanding-results)