benchos-bigbac-assembler

name	benchos-bigbac-assembler
description	Assemble BenchOS demo multi-insert multi-insert constructs, compute HiFi assembly reaction volumes, and export the final assembled sequence. Use when the user wants a BenchOS CLI or agent-driven version of the BigBac Assembler tool.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli`, `benchos-cli`, and the curated `python-basic` capability pack.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS BigBac Assembler

Use this skill when the user wants to:

• assemble one to five inserts into a BenchOS pBIG1 vector
• compute HiFi assembly input volumes from insert concentrations
• resolve accession-like insert inputs before assembly
• export the final assembled sequence and JSON summary into the BenchOS workspace

Browser Tool

BenchOS also exposes this workflow in the website Tools page as BigBac Assembler. Use the browser tool for interactive editing and quick copy/download work; use this skill for agent-driven execution and saved artifacts.

Quick Rules

• Use the shared wrapper script rather than re-implementing the BenchOS demo multi-insert assembly logic inline.
• Accept one to five inserts.
• Each insert input can be a raw DNA sequence or an accession-like identifier.
• Keep outputs under artifacts/bigbac/<run-name>/ when possible.
• Treat the assembly mix heuristic as the current BenchOS toolkit convention, not a generalized cloning protocol engine.

Default Workflow

1. Confirm the pBIG1 vector, vector concentration, and each insert source plus concentration.
2. Install the capability pack:

{ "args": ["capabilities", "install", "--name", "python-basic"] }

3. Run the shared script:

{
  "args": [
    "exec",
    "--capability",
    "python-basic",
    "--cwd",
    ".",
    "--",
    "/opt/benchos/shared-skills/benchos-bigbac-assembler/scripts/bigbac_assembler_cli.py",
    "--vector",
    "a",
    "--vector-concentration",
    "100",
    "--insert-source",
    "NM_001256789",
    "--insert-concentration",
    "50",
    "--insert-source",
    "ATGGCC...",
    "--insert-concentration",
    "40",
    "--output-dir",
    "artifacts/bigbac/run-001",
    "--json"
  ]
}

4. Read bigbac-assembly.json and report the insert volumes, final reaction setup, and assembled sequence length.
5. If the user wants the sequence elsewhere in BenchOS, attach or append the generated FASTA through the normal entry or registry APIs.

Outputs

• bigbac-assembly.json: structured result payload
• bigbac-assembly.fasta: assembled DNA sequence

Notes

• The script bundles the BenchOS demo multi-insert sequence asset inside the shared skill so CLI behavior stays deterministic.
• Accession resolution uses NCBI nucleotide FASTA fetch before assembly.