SlopGene

A free, open-source and scriptable plasmid and sequence editor for Windows, macOS and Linux.

SlopGene on GitHub: source code, documentation and older versions.

Sample Workflow

Restriction cloning

Cutting GFP out of pGFP with EcoRI and BamHI and putting it into pDoom, step by step on the bench

Cloning by PCR

Copying mCherry out of pCherry by PCR with EcoRI and BamHI tails, and putting it into pDoom

Checking sequencing results

Aligning a whole-plasmid sequencing read of a pDoom colony to its map: every difference is marked on the map and in the bases, with its effect on the protein

Command line and scripts

SlopGene also enables powerful automated cloning workflows by exposing everything in the app through the slopgene command line and a scripting language, with JSON output for pipelines and AI agents.

// The restriction cloning above, as a script. The protocol it writes opens in the app as the bench.
protocol_new("clone.json", "pDoom.dna", "pGFP.dna", #{ cut_out: "GFP", enzymes: "EcoRI,BamHI" });

Run it with slopgene run clone.rhai. The scripting guide lists every function.