> ## 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.

# Presets Reference

> Pre-configured parameter sets for common PCR applications

PrimerLab includes optimized presets for common PCR applications. Presets provide pre-configured parameters that you can use as-is or customize.

## Viewing Presets

```bash theme={null}
# List all available presets
primerlab preset list

# Show details of a specific preset
primerlab preset show long_range
```

***

## Available Presets

### Standard Presets

| Preset           | Amplicon Size | Tm Range |  QC Mode | Best For               |
| ---------------- | :-----------: | :------: | :------: | ---------------------- |
| `standard_pcr`   |  100-1000 bp  |  57-63°C | standard | General research       |
| `diagnostic_pcr` |   80-200 bp   |  58-62°C |  strict  | Clinical testing       |
| `long_range`     | 3000-10000 bp |  62-68°C |  strict  | Large gene fragments   |
| `cloning_pcr`    |  200-3000 bp  |  58-68°C | standard | Molecular cloning      |
| `sequencing_pcr` |   300-800 bp  |  58-62°C | standard | Sanger sequencing      |
| `dna_barcoding`  |   400-700 bp  |  50-60°C |  relaxed | Species identification |
| `rt_pcr`         |   80-150 bp   |  58-62°C |  strict  | Reverse transcription  |

***

## Preset Details

### `diagnostic_pcr`

High-specificity primers for clinical/diagnostic applications.

**Use Cases**: Pathogen detection, genetic testing, point-of-care

| Parameter    | Value               |
| ------------ | ------------------- |
| Primer Size  | 20-28 bp (opt: 22)  |
| Tm           | 58-62°C (opt: 60°C) |
| GC%          | 45-55%              |
| Product Size | 80-200 bp           |
| QC Mode      | strict              |

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

***

### `long_range`

Optimized for amplifying long DNA fragments (3-10+ kb).

**Use Cases**: Full-length gene amplification, large deletions, genomic regions

| Parameter    | Value               |
| ------------ | ------------------- |
| Primer Size  | 25-35 bp (opt: 28)  |
| Tm           | 62-68°C (opt: 65°C) |
| GC%          | 40-60%              |
| Product Size | 3000-10000 bp       |
| QC Mode      | strict              |

> **Note**: Requires specialized polymerases (e.g., LA Taq, LongAmp).

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

***

### `cloning_pcr`

Primers designed for molecular cloning with restriction sites.

**Use Cases**: Gene cloning, subcloning, expression vector construction, Gibson assembly

| Parameter    | Value               |
| ------------ | ------------------- |
| Primer Size  | 25-40 bp (opt: 30)  |
| Tm           | 58-68°C (opt: 62°C) |
| GC%          | 40-60%              |
| Product Size | 200-3000 bp         |
| QC Mode      | standard            |

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

***

### `dna_barcoding`

DNA barcoding applications (COI, rbcL, ITS, etc.).

**Use Cases**: Species identification, biodiversity surveys, phylogenetics

| Parameter    | Value               |
| ------------ | ------------------- |
| Primer Size  | 20-28 bp (opt: 23)  |
| Tm           | 50-60°C (opt: 55°C) |
| GC%          | 35-70%              |
| Product Size | 400-700 bp          |
| QC Mode      | relaxed             |

> **Note**: Relaxed mode allows for diverse templates across taxa.

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

***

### `rt_pcr`

Reverse transcription PCR for cDNA amplification.

**Use Cases**: Gene expression analysis, mRNA detection

| Parameter    | Value     |
| ------------ | --------- |
| Primer Size  | 18-25 bp  |
| Tm           | 58-62°C   |
| Product Size | 80-150 bp |
| QC Mode      | strict    |

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

***

## Using Presets

### In Configuration File

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

input:
  sequence_path: ./my_gene.fasta

# Override specific parameters if needed
parameters:
  tm:
    opt: 62.0  # Override default 60°C
```

### Via CLI

```bash theme={null}
# Use preset directly
primerlab run pcr --preset diagnostic_pcr --sequence gene.fasta
```

***

## Customizing Presets

Presets provide defaults, but you can override any parameter:

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

# Your overrides take precedence
parameters:
  product_size_range: [[5000, 15000]]  # Extend range
  tm:
    opt: 68.0  # Higher Tm for very long amplicons

qc:
  mode: relaxed  # Override strict to relaxed
```

***

## See Also

* [Configuration Reference](config)
* [Customization Guide](/docs/guides/customization)
* [CLI Reference](cli)