Related papers: Sequence assembly from corrupted shotgun reads
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
We consider the problem of reconstructing graphs or labeled graphs from neighborhoods of a given radius r. Special instances of this problem include the well known: DNA shotgun assembly; the lesser-known: neural network reconstruction; and…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…