Related papers: Sequence assembly from corrupted shotgun reads
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
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…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…