benchos-cloning

name	benchos-cloning
description	Decision trees and workflows for molecular cloning in structural biology labs. Use when the user asks about LIC vs Gibson, construct design, tag strategy, codon optimization planning, multi-subunit assembly, or clone verification workflow.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli` and the related BenchOS sequence-design/integration skills when execution is needed.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS Cloning

Use this skill for cloning strategy and decision support. This is a guidance skill: it helps choose the expression system, cloning method, and validation path, then routes execution into the relevant BenchOS skills.

Core Rules

• Prefer LIC first for standard vector systems; switch to Gibson/HiFi when LIC fails or the construct demands it.
• For larger proteins or multi-subunit assemblies, bias toward insect-cell expression.
• For multi-subunit complexes, prefer a single-plasmid biGBac strategy when practical.
• Verification standard is strict: only 100% identity to the intended construct passes.

Routing

• For baculovirus workflow details, use benchos-insect-cell.
• For codon optimization execution, use benchos-codon-optimize.
• For plasmid-map parsing and encoded-protein extraction, use benchos-snapgene.
• For sequencing retrieval, use benchos-plasmidsaurus.

BenchOS Workflow

1. Decide expression system from size, complexity, and precedent.
2. Choose cloning method and tag placement.
3. Decide whether the insert comes from PCR or synthesis.
4. Verify the plasmid or final construct before recording it in BenchOS.