Abstract
BackgroundHigh-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.ResultLevenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.ConclusionWe present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.
Highlights
High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research
We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations
Any randomly picked synthetic nucleotide sequence can be used as a barcode, this approach is problematic because all basic parameters of the corresponding oligonucleotide, namely minimal distance, GC content, sequence redundancy etc. cannot be properly controlled [13]
Summary
High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected This can be accomplished by implementing error correcting algorithms and codes. Since modern machines are (at the time of writing this manuscript) capable of generating up to 8 ∗ 109 base pairs (8 Gbp) total read length in one lane, In such cases many samples are combined in a single batch and sequenced as one sample Using this multiplexed format, specific sample tags, called barcodes, are added to the amplification or sequencing primer to discriminate all sub-samples in the mixture. The protocol is efficient as long as barcodes can be read robustly [9] It is known, that multiple errors can occur with DNA sequencing due to defects in primer synthesis, the ligation process, sample pre-amplification, and sequencing. Any randomly picked synthetic nucleotide sequence can be used as a barcode, this approach is problematic because all basic parameters of the corresponding oligonucleotide, namely minimal distance, GC content, sequence redundancy etc. cannot be properly controlled [13]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
