User Guide

User Guide

This guide explains how to install and run insilicoPCR from the portable releases.

Download and extract

1. Open the GitHub Releases page.
2. Download the archive for your operating system:
   • Linux: insilicoPCR-<version>-linux-x64.zip
   • Windows: insilicoPCR-<version>-windows-x64.zip
3. Extract the ZIP archive to a writable folder.
4. Keep the extracted folder intact. Do not move files out of the release folder.

Portable releases include:

• insilicoPCR
• OpenJDK 26 runtime
• JavaFX 26.0.1 runtime
• BBMap
• NCBI BLAST+
• platform launchers

No separate Java, JavaFX, BBMap, or BLAST+ installation is required.

Starting the graphical application

Linux

Open a terminal in the extracted release folder and run:

chmod +x run-insilicoPCR.sh
./run-insilicoPCR.sh

Running from a terminal is recommended on Linux because startup messages and errors are displayed directly in the console.

Windows

Open the extracted release folder and double-click:

run-insilicoPCR.bat

You can also run it from PowerShell:

.\run-insilicoPCR.bat

Inputs

insilicoPCR accepts genome assemblies and sequencing reads.

Supported examples:

• .fasta
• .fa
• .fna
• .fastq
• .fq

The input can be one sequence file or a directory containing sequence files.

Primer file

The primer file must be a FASTA file using the special primer nomenclature described in Primer FASTA Format.

Standard PCR and qPCR mode

Run standard PCR assays and qPCR/probe assays separately.

• Standard PCR assays use -F and -R entries.
• qPCR/probe assays use -F, -R, and -P entries.

Do not mix assays with probes and assays without probes in the same primer FASTA file.

Outputs

A typical run creates output files such as:

• quality/runtime logs
• detailed per-sample results
• consolidated reports
• Excel reports
• files used by the synthetic gel visualizer

Synthetic gel visualizer

After a run completes, use the gel viewer button in the GUI to inspect a gel-like representation of the consolidated report.

The gel viewer can also open previous run folders or consolidated report TSV files when available. See Synthetic Gel Visualizer.

Troubleshooting

If the application does not start:

• Make sure the ZIP was fully extracted.
• Make sure you downloaded the correct release for your operating system.
• On Linux, run the launcher from a terminal.
• On Linux, run chmod +x run-insilicoPCR.sh if needed.
• Keep the runtime/ directory beside the launcher.
• On Windows, SmartScreen may warn about unsigned software. Only continue if the release was downloaded from the official repository.