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insilicoPCR Wiki

Welcome to the insilicoPCR Wiki.

This is the detailed documentation for users and developers. The repository README is intentionally compact; the Wiki should be the main manual for installing, running, troubleshooting, and developing the application.

This docs/wiki/ directory is a source-controlled mirror of the GitHub Wiki content. Once the GitHub Wiki is initialized, these pages can be copied or pushed into the insilicoPCR.wiki repository.

Getting Started

• Installation
• Portable Releases
• First Analysis

User Guide

• GUI Overview
• Running Analyses
• Primer FASTA Format
• Standard PCR vs qPCR
• Reports
• Synthetic Gel Visualizer
• Command-line Interface
• Troubleshooting
• FAQ

Developer Guide

• Developer Guide
• Architecture
• Runtime Layout
• Build System
• Release Pipeline
• Contributing

What insilicoPCR does

insilicoPCR performs in silico PCR analysis against genome assemblies and sequencing reads.

Supported input types include:

• genome assemblies: .fasta, .fa, .fna
• sequencing reads: .fastq, .fq
• directories containing multiple FASTA or FASTQ files

The application supports both:

• a JavaFX graphical desktop interface
• a command-line interface for batch runs and pipelines

Portable releases include Java, JavaFX, BBMap, and NCBI BLAST+, so end users do not need to install these tools separately.