Design of short barcodes for next generation sequencing of DNA and RNA

Schober, Steffen; Mir, Katharina; Neuhaus, Klaus; Bossert, Martin

doi:10.1109/gensips.2012.6507719

Cited by 3 publications

(2 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The types of errors and the error rates vary among next generation sequencing platforms [ 4 , 19 – 24 ]. Recently, researchers have constructed sequence tags using error correction schemes, which are more robust to synthesis, replication, and sequencing errors (i.e., minimizing crossover and loss), while also allowing the correction of certain types of errors [ 1 – 4 , 12 , 13 , 25 , 26 ]. Hamming codes [ 27 ] are used widely to design DNA tags.…”

Section: Introductionmentioning

confidence: 99%

“…Costea et al proposed the DNA-based tag generator and demultiplexor (TagGD), which is a fully-customizable, rapid, and accurate software package that can generate thousands of barcodes to satisfy user-defined constraints and guarantee full demultiplexing accuracy [ 25 ]. Schober et al proposed a simple randomized method for constructing barcodes with better error-correcting capabilities compared with previous methods [ 26 ]. Recently, Buschmann and Bystrykh adapted the Levenshtein distances by considering the DNA context where the length of the new mutated barcode in the sequence read was identified correctly [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Improved Lower Bounds of DNA Tags Based on a Modified Genetic Algorithm

et al. 2015

View full text Add to dashboard Cite

The well-known massively parallel sequencing method is efficient and it can obtain sequence data from multiple individual samples. In order to ensure that sequencing, replication, and oligonucleotide synthesis errors do not result in tags (or barcodes) that are unrecoverable or confused, the tag sequences should be abundant and sufficiently different. Recently, many design methods have been proposed for correcting errors in data using error-correcting codes. The existing tag sets contain small tag sequences, so we used a modified genetic algorithm to improve the lower bound of the tag sets in this study. Compared with previous research, our algorithm is effective for designing sets of DNA tags. Moreover, the GC content determined by existing methods includes an imprecise range. Thus, we improved the GC content determination method to obtain tag sets that control the GC content in a more precise range. Finally, previous studies have only considered perfect self-complementarity. Thus, we considered the crossover between different tags and introduced an improved constraint into the design of tag sets.

show abstract