# title
OBGene: Optimal Barcode Generator for NGS Experiments

# abstract
We are addressing a fundamental problem in the selection of optimal sets of DNA barcodes to be used in multiplexing of samples in a next-generation sequencing (NGS) through an optimization framework called OBGene. We define a constrained-optimization setting whose cost function and constraints utilize the notion of Hamming distance between barcodes and the experimental requirements, respectively. We consider diverse possible constraints that might be imposed by a practitioner; for example, maximum distance between barcodes, balanced list, and a desired limit for the GC-content. Owing to the size of the search space, we propose to use a stochastic search algorithm, ICA, to find the global optima of the cost function. As a numerical example, we provide a list of 20 barcodes through the simulation.  2012 IEEE.

# publicationVenue.label
IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics

# publicationOutlet
2012 IEEE INTERNATIONAL WORKSHOP ON GENOMIC SIGNAL PROCESSING AND STATISTICS (GENSIPS)

# nameOfConference
Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

# publisher.label
Institute of Electrical and Electronics Engineers (IEEE)

# authorList[]
Atashpaz-Gargari, E., Esfahani, M. S., Metz, R., & Johnson, C. D.