Low-complexity and highly robust barcodes for error-rich single molecular sequencing

Hardware Acceleration of Identifying Barcodes in Multiplexed Nanopore Sequencing

“…Therefore, DNA barcodes need to be designed to resist insertion, deletion, and substitution errors, which is important for improving the sequencing accuracy of NGS. Aiming at various types of errors introduced during multiplexed nanopore sequencing, a new DNA barcode construction scheme was proposed in [12], which combined a pseudorandom sequence with a cyclic block code and converted them into bases by bit pairs. Here, the pseudorandom sequence acted as a hidden component of sequencing barcodes to identify indels and the cyclic block code was used against the substitution errors.…”

“…Sequencing barcode identification scheme based on cyclic shifting and DP algorithm [12]. (Reprinted with permission from ref.…”

“…Conventional construction and identification methods for DNA barcodes are based on Hamming distance [7,8], Levenshtein distance [9,10], watermark code [11], etc. Recently, in [12], a scheme that combines a pseudorandom sequence with a cyclic block code was proposed to construct barcodes while the cyclic shifting and DP algorithm were used to identify barcodes. This scheme had the advantages of a low complexity and high robustness.…”

“…Compared to central processing units (CPUs), FPGAs provide a higher bit-level data parallelism and can customize hardware according to the requirements, which leads to a higher computing speed [16,17]. Therefore, taking the scheme proposed in [12] as an example, this paper designs and implements an FPGA-based hardware accelerator.…”

“…This section reviews the related works, including the barcode identification scheme proposed in [12] and the DP algorithm for identifying an insertion/deletion (indel).…”