Overcoming High Nanopore Basecaller Error Rates for DNA Storage Via Basecaller-Decoder Integration and Convolutional Codes

Chandak, Shubham; Neu, Joachim; Tatwawadi, Kedar; Mardia, Jay; Lau, Billy T.; Kubit, Matthew; Hulett, Reyna; Griffin, P.B.; Wootters, Mary; Weissman, Tsachy; Ji, Hanlee P.

doi:10.1101/2019.12.20.871939

Cited by 16 publications

(21 citation statements)

References 37 publications

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“…One should also note about perspectives of using of DNA as an ultrahighdensity storage medium that could meet exponentially growing worldwide demand for archival data storage [Banal et al, 2021;Chandak et al, 2019]. Our results about algebraic features of DNA informatics can help in solving some engineering problems in this technological challenge.…”

Section: Some Concluding Remarksmentioning

confidence: 80%

Algebraic Rules for the Percentage Composition of Oligomers in Genomes

Petoukhov¹

2021

Preprint

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The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author considers genomic DNA nucleotide sequences as multilayers sequences of n-plets and studies the percentage contents of n-plets in different layers. Unexpected rules of invariance of total sums of percentages in certain tetra-groupings of n-plets in different layers of genomic DNA sequences are revealed. These discovered rules are candidates for the role of universal genomic rules. A tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets is used in the study. This matrix approach allows revealing algebraic properties of the mentioned genetic rules of probabilities, which are useful for developing algebraic and quantum biology. Some analogies of the discovered genetic phenomena with phenomena of Gestalt psychology are noted and discussed. The author connects the received results about the genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Additional attention is paid to the algebraic features of the system of structured DNA alphabets and their relationship with the methods of algebraic holography, known in the technique of processing discrete signals. The concept of algebraic-holographic genetics is being developed for the understanding of inherited holographic properties of organisms.

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Section: Some Concluding Remarksmentioning

confidence: 80%

Algebraic Rules for the Percentage Composition of Oligomers in Genomes

Petoukhov¹

2021

Preprint

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“…After, the remaining reads are decoded and the corrupted ones discarded. One of the latest works [4] addresses the high error rate in the nanopore reads by integrating a Viterbi error correction decoder with the basecaller and using convolutional codes.…”

Section: Introductionmentioning

confidence: 99%

Decoding Of Nanopore-Sequenced Synthetic DNA Storing Digital Images

Antonio

Dimopoulou

Antonini

et al. 2021

2021 IEEE International Conference on Image Processing (ICIP)

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Digital media explosion has led to an exponential increase of the amount of data generated worldwide and the need for new means of storage able to keep up with the current growth of digital information has become a critical challenge. During the last decade, DNA has been proven to be a potential candidate thanks to its biological properties allowing to store information at high density (215 petabytes in 1 gram) for centuries.In previous works we have presented an end-to-end storage workflow specifically designed for the efficient storage of images onto synthetic DNA and proven its feasibility in a wetlab experiment in which sequencing was performed using the Illumina machine. In this work we are studying the sequencing using rather the MinION sequencer on the same data after being stored in a sealed capsule for two years. MinION is a very promising sequencer although introducing a much higher error rate in the process of reading. In this paper, we propose a solution to deal with the MinION sequencing noise allowing to recover the original stored data.

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“…DNA storage channel models currently used for error-correction performance evaluation either assume nonrealistic independent and identically distributed (i.i.d.) errors [6], or rely on Deep-Learning approaches [7], which makes them difficult to interpret.…”

Section: Introductionmentioning

confidence: 99%