barcodeEZ¶
barcodeEZ is a Python package for designing complex, combinatorial DNA barcode libraries for molecular cloning.
The package allows design and creation of a site-aware Barcodes object. It is built around sites, expandable positions, restriction-enzyme boundaries, optimized overhangs, and optional fixed sequences. BarcodeEZ draws orthogonal barcode sequence from a prebuilt corpus, assembles forward and reverse oligos, screens them for unwanted sequence content, and exports a ready-to-order oligo pool.
What it does¶
- Design a library structure from restriction-enzyme boundaries — use the built-in default panel or supply your own enzymes.
- Add positions within each site for combinatorial, multi-position barcoding (up to 8 positions per site), with automatically assigned optimized internal overhangs.
- Generate barcodes of any length from a corpus of ~30,000 orthogonal 60-mers shipped with the package.
- Attach fixed sequences to either end of a site.
- Validate against restriction sites and undesired motifs, automatically swapping out any contaminated barcode.
- Inspect the whole design as a pandas DataFrame.
- Export a single-stranded oligo order form as CSV.
A minimal example¶
from barcodeEZ import Barcodes
b = Barcodes(n_sites=2) # two barcoded sites, default enzymes
b.generate_barcodes(bc_len=20, n_barcodes=96)
b.validate() # screen + replace contaminated barcodes
b.write_order_form('library.csv') # export the oligo pool