> ## 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.

# PrimerLab Documentation

> Modular bioinformatics framework for automated primer and probe design

**PrimerLab** is a modular bioinformatics framework for automated primer and probe design.

## Quick Links

* **[Quick Start](/docs/guides/quickstart)**: Design your first primers in 5 minutes.
* **[Guides](/docs/guides/index)**: Step-by-step tutorials for PCR, qPCR, and more.
* **[Reference](/docs/reference/cli)**: CLI commands, API docs, and configuration.
* **[Concepts](/docs/concepts/index)**: Learn about scoring, algorithms, and quality control.

***

## Installation

```bash theme={null}
pip install primerlab-genomic
```

Verify installation:

```bash theme={null}
primerlab --version
primerlab health
```

***

## Key Features

| Feature                 | Description                                 |
| ----------------------- | ------------------------------------------- |
| **PCR Design**          | Standard primer design with quality control |
| **qPCR Design**         | TaqMan and SYBR Green assay design          |
| **In-silico PCR**       | Virtual amplification validation            |
| **Off-target Check**    | BLAST-based specificity analysis            |
| **Batch Processing**    | Multi-sequence design                       |
| **Species Specificity** | Cross-reactivity testing                    |

***

## Quick Example

```bash theme={null}
# Create configuration
cat > my_config.yaml << 'EOF'
input:
  sequence_path: ./gene.fasta
parameters:
  tm:
    opt: 60.0
  product_size:
    min: 150
    max: 300
EOF

# Design primers
primerlab run pcr --config my_config.yaml
```

***

## Architecture

PrimerLab uses a three-tier design:

```mermaid theme={null}
graph LR
    CLI[CLI] --> Workflow[Workflows]
    API[Python API] --> Workflow
    Workflow --> Core[Core Utilities]
    Core --> P3[Primer3]
    Core --> BLAST[BLAST+]
```

Learn more: [System Architecture](/docs/concepts/architecture)

***

## Version

Current version: **v1.0.1**

See [Changelog](/docs/changelog) for version history.

***

## Links

* [GitHub Repository](https://github.com/engkinandatama/primerlab-genomic)
* [PyPI Package](https://pypi.org/project/primerlab-genomic/)
* [DeepWiki Docs](https://deepwiki.com/engkinandatama/primerlab-genomic)