Insertion and deletion correcting DNA barcodes based on watermarks

Abstract

BackgroundBarcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequencing procedure. A post-processing step is needed to sort the sequencing data according to their origin, utilizing these DNA labels. The final separation step is called demultiplexing and is mainly determined by the characteristics of the DNA code words used as labels.Currently, we are facing two different strategies for barcoding: One is based on the Hamming distance, the other uses the edit metric to measure distances of code words. The theory of channel coding provides well-known code constructions for Hamming metric. They provide a large number of code words with variable lengths and maximal correction capability regarding substitution errors. However, some sequencing platforms are known to have exceptional high numbers of insertion or deletion errors. Barcodes based on the edit distance can take insertion and deletion errors into account in the decoding process. Unfortunately, there is no explicit code-construction known that gives optimal codes for edit metric.ResultsIn the present work we focus on an entirely different perspective to obtain DNA barcodes. We consider a concatenated code construction, producing so-called watermark codes, which were first proposed by Davey and Mackay, to communicate via binary channels with synchronization errors. We adapt and extend the concepts of watermark codes to use them for DNA sequencing. Moreover, we provide an exemplary set of barcodes that are experimentally compatible with common next-generation sequencing platforms. Finally, a realistic simulation scenario is use to evaluate the proposed codes to show that the watermark concept is suitable for DNA sequencing applications.ConclusionOur adaption of watermark codes enables the construction of barcodes that are capable of correcting substitutions, insertion and deletion errors. The presented approach has the advantage of not needing any markers or technical sequences to recover the position of the barcode in the sequencing reads, which poses a significant restriction with other approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0482-7) contains supplementary material, which is available to authorized users.

Designing robust watermark barcodes for multiplex long-read sequencing

“…This comes as no surprise, since most existing SMRT-CCS barcodes are obtained by imposing a minimum edit distance constraint to sets of random sequences [2], a design method known to scale poorly with increasing barcode length [18]. To overcome the limitations of random barcodes in general multiplex SMRT sequencing applications, systematic barcodes can be alternatively explored.Recently, watermark barcodes, a class of systematic barcodes able to deal with sequencing indels and substitutions, have been proposed [15]. These are inspired in the design of watermark error correcting codes [5], originally developed to deal with synchronization and substitution errors in digital communications.…”

“…Since the watermark is known to the decoder, this similarity provides a means to maintain synchronization in the presence of random insertions and deletions. Substitution errors which remain after achieving synchronization are dealt with through regular error correction, making use of available redundancy.Although watermark barcodes appear promising, their practical design for sequencing applications remains an open problem: for SMRT-CLR sequencing error rates, even the best barcodes reported in [15] yield sample misassignment rates in the vicinity of 5%. In this paper, we revisit the design of DNA barcodes around the watermark concept.…”

“…In this paper, we revisit the design of DNA barcodes around the watermark concept. As opposed to [15], we consider short low-density parity check (LDPC) codes [17] as outer codes, which offer the interesting possibility of discarding very noisy reads rather than risk erroneous decoding. In addition, as our main contribution, the key watermark-carrier imprinting that conveys resilience to challenging insertion and deletion errors is modified so that non-sparse carriers are now allowed.…”

“…Recently, watermark barcodes, a class of systematic barcodes able to deal with sequencing indels and substitutions, have been proposed [15]. These are inspired in the design of watermark error correcting codes [5], originally developed to deal with synchronization and substitution errors in digital communications.…”

“…Although watermark barcodes appear promising, their practical design for sequencing applications remains an open problem: for SMRT-CLR sequencing error rates, even the best barcodes reported in [15] yield sample misassignment rates in the vicinity of 5%. In this paper, we revisit the design of DNA barcodes around the watermark concept.…”