Coded Shotgun Sequencing

Ravi, Aditya Narayan; Vahid, Alireza; Shomorony, Ilan

doi:10.1109/jsait.2022.3151737

Cited by 7 publications

(5 citation statements)

References 31 publications

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“…X kn } of reads resulting from this sampling process is the channel output. The following theorem, presented in [24], establishes the capacity of this channel.…”

Section: B Capacity Of the Shotgun Sequencing Channelmentioning

confidence: 99%

“…This scheme, analyzed in a careful way, can be used to show that all rates R < C SSC are achievable. The full details of this proof are available in [24]. We point out that this coding scheme is also based on random coding and is therefore computationally very expensive, just as in the TPC case.…”

Section: B Capacity Of the Shotgun Sequencing Channelmentioning

confidence: 99%

“…Under the scaling we choose (K = cn/L and L = L log n), the total fraction of bits (in the codeword) sequenced by the SSC is 1 − e −c as n → ∞ [24]. Therefore the total fraction of bits erased will be e −c , as n → ∞, and we can choose the rate of the erasure code to be R er = 1 − e −c .…”

Section: Letmentioning

confidence: 99%

“…The two channel models we will consider are inspired by the aforementioned practical considerations (1) and ( 2) and are illustrated in Figure 2. We refer to these two channels as the Torn-Paper Channel (TPC) [20][21][22], shown in Figure 2(a), and the Shotgun Sequencing Channel (SSC) [23,24], shown in Figure 2(b). The TPC breaks the input sequence x n into pieces of random sizes, and a subset of these pieces is observed at the output.…”

Section: Introductionmentioning

confidence: 99%

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An Information Theory for Out-of-Order Media With Applications in DNA Data Storage

Ravi,

Vahid,

Shomorony

2024

IEEE Trans. Mol. Biol. Multi-Scale Commun.

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Recent advancements in DNA-based storage prototypes focus on encoding information across multiple DNA molecules. This approach utilizes high-throughput sequencing technologies, leading to outputs that are out-of-order. We study the shuffling channel, where input codewords are split into fixed-size fragments. We show that achieving channel capacity uses index-based coding, which assigns unique indices to each fragment. We also introduce two more complex channels, which aim to model popular sequencing strategies in DNA sequencing. In the torn-paper channel, the input codeword is torn up into fragments of random sizes, while in the shotgun sequencing channel, fixed-length random substrings of the input codeword are observed at the output. In both of these channels, the lack of ordering cannot be circumvented by simply adding unique indices to the fragments. We show how the capacity of both of these channels can be achieved using random codes. We introduce and analyze code constructions based on index sequences. While these codes are computationally efficient, they are not capacityachieving, and we leave the questions of finding efficient capacityachieving codes for these settings as open problems.

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“…X kn } of reads resulting from this sampling process is the channel output. The following theorem, presented in [24], establishes the capacity of this channel.…”

Section: B Capacity Of the Shotgun Sequencing Channelmentioning

confidence: 99%

Section: B Capacity Of the Shotgun Sequencing Channelmentioning

confidence: 99%

Section: Letmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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An Information Theory for Out-of-Order Media With Applications in DNA Data Storage

Ravi,

Vahid,

Shomorony

2024

IEEE Trans. Mol. Biol. Multi-Scale Commun.

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“…The problem at hand is similar to that of shotgun DNA sequencing, in which a large number of short reads from random locations in the DNA sequence are assembled together, rather than attempting to sequentially read the entire genome of the organism [23]. However, solutions for this problem consider large sequences, which is not our case and at least in the context of this work, parallel readings of the sequence are not viable as we would need multiple cameras.…”

Section: Introductionmentioning

confidence: 99%

Frame recovery using multiple images in rolling shutter based systems

Rego

Pérez

Fonseca

et al. 2023

IET Optoelectronics

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An algorithm for recovering transmitted static identifiers (IDs) in rolling shutter based Optical Camera Communication systems is proposed by the authors, considering a system comprised of a camera and a circular light source. The goal is to allow the correct decoding when the ID frame is only partially detected in the image. A baseline algorithm as reference for the frame recovery success rate (FRSR) and a reconstruction algorithm based on the idea of capturing multiple frame fragments and reassembling them is proposed in order to recover the transmitted ID not entirely seen on a single image. It was proven, by simulation, that the maximum distance at which the IDs recovery can be guaranteed is increased by 2.5 fold with the proposed algorithm, for 6‐bit, 8‐bit and 10‐bit codewords. An experimental validation algorithm was also proposed, using image processing techniques to extract the bitstreams and test the ID recovery process. The proposed algorithm improves the FRSR for a given distance, even in the presence of considerable bit errors in the bitstreams extracted from the images.

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