title: Short barcodes for next generation sequencing.
abstract: We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.
authors.affiliation: Institute of Communications Engineering, Ulm University, Ulm, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Mir
authors.affiliation: Chair for Microbial Ecology, Technische Universität München, Freising, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Neuhaus
authors.affiliation: Institute of Communications Engineering, Ulm University, Ulm, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Bossert
authors.affiliation: Institute of Communications Engineering, Ulm University, Ulm, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Schober
mesh_terms: D004247:DNA / Q000737:chemistry*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA