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2015 ; 10
(10
): e0140459
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DNA Barcoding through Quaternary LDPC Codes
#MMPMID26492348
Tapia E
; Spetale F
; Krsticevic F
; Angelone L
; Bulacio P
PLoS One
2015[]; 10
(10
): e0140459
PMID26492348
show ga
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).
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