Coding for Trace Reconstruction over Multiple Channels with Vanishing Deletion Probabilities

by   Serge Kas Hanna, et al.

Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each bit of the input codeword š±āˆˆ{0,1}^n independently with probability p. We focus on the regime where the deletion probability p ā†’ 0 when nā†’āˆž. Our main contribution is designing a novel code for trace reconstruction that allows reconstructing a coded sequence efficiently from a constant number of traces. We provide theoretical results on the performance of our code in addition to simulation results where we compare the performance of our code to other reconstruction techniques in terms of the edit distance error.


page 1

page 2

page 3

page 4

āˆ™ 08/12/2019

Coded trace reconstruction in a constant number of traces

The coded trace reconstruction problem asks to construct a code CāŠ‚{0,1}^...
āˆ™ 07/14/2021

Trellis BMA: Coded Trace Reconstruction on IDS Channels for DNA Storage

Sequencing a DNA strand, as part of the read process in DNA storage, pro...
āˆ™ 05/20/2019

Coding for Deletion Channels with Multiple Traces

Motivated by the sequence reconstruction problem from traces in DNA-base...
āˆ™ 03/24/2019

Coded trace reconstruction

Motivated by average-case trace reconstruction and coding for portable D...
āˆ™ 05/29/2020

Algorithms for reconstruction over single and multiple deletion channels

Recent advances in DNA sequencing technology and DNA storage systems hav...
āˆ™ 10/12/2020

Trace Reconstruction Problems in Computational Biology

The problem of reconstructing a string from its error-prone copies, the ...
āˆ™ 02/10/2021

Trace Reconstruction with Bounded Edit Distance

The trace reconstruction problem studies the number of noisy samples nee...

Please sign up or login with your details

Forgot password? Click here to reset