DNA Barcoding through Quaternary LDPC Codes

Abstract

For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10−2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10−9 at the expense of a rate of read losses just in the order of 10−6.

Designing robust watermark barcodes for multiplex long-read sequencing

“…Instead, we preserve the original formulation of watermark codes relying on powerful low-density parity check (LDPC) codes [17]. In particular, we use short quaternary LDPC codes developed in [20] for DNA barcoding applications affected mainly by substitution errors. These can be easily extended to arbitrary order fields, unlike the codes collected in [9], which are currently limited to F 9 .…”

“…Given these likelihoods, generic linear codes can be decoded using Maximum-Likelihood (ML) approaches, which select the codeword that maximizes the probability of receiving r. While this is mathematically optimal, there always exists a codeword which maximizes such probability and, thus, decoding never fails. As noted in [20], incomplete decoders (i.e. decoders that report a decoding failure when the result is ambiguous) can be used instead to control the trade-off between detected errors (read losses) and undetected errors (sample misassignments).…”

Robust and scalable barcoding for massively parallel long-read sequencing

“…Several authors 1 – 3 early recognized that the former challenge is analogous to the issue of reliable transmission of information in the presence of noise. This a well-studied problem in the field of Information Theory 4 , where different approaches have been proposed.…”

An optimized initialization for LDPC decoding over GF(q) in impulsive noise environments

“…To avoid bit errors in data transmission, it is an efficient way to employ low density parity check (LDPC) codes in navigation satellite communication channel. Nowadays, LDPC codes have been widely applied in the 2nd-generation digital video broadcast via satellite (DVB-S2) standard [ 5 ], 5G mobile communications [ 6 ], DNA barcoding [ 7 ], as well as the uplink of mobile satellite communication [ 8 ].…”