Barcode Generator - Nanopore

Barcode generator tailored for nanopore sequencing.

Features:

• No homopolymers
• GC-content between 40-60% (can be changed manually in the code)
• Distance threshold in Levenshtein
• Custom barcode length
• Custom number of barcodes

Work in progress

• Custom GC-content setting

Known issues:

• When the distance threshold is approximatly half of the barcode length or longer, generating more than 10 barcodes will be costly, in some cases impossible.

Getting Started

Installation of prerequisites

• Python3
• Levenshtein package for python (pip for install)
• Progress package - used for verbose output

Installing Levenshtein-package:

pip3 install python-levenshtein

Installing progress package:

pip3 install progress

Running the script

python3 barcode_gen.py

Several options are available, check them using the -h och --help flag:

python3 barcode_gen.py -h

Authors

• Alice Anlind

Acknowledgments

• Vidilab's slack channel for RnD for suggestions of improvements