相关论文: Barnacle: An Assembly Algorithm for Clone-based Se…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
(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…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
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…
Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources. In this study, we present an efficient de…
This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Most existing 3D assembly methods treat the problem as pure pose estimation, rearranging observed parts via rigid transformations. In contrast, human assembly naturally couples structural reasoning with holistic shape inference. Inspired by…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using "bubble" structures within the de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding…
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…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…