相关论文: Simulating the DNA String Graph in Succinct Space

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…

Subgraph counting aims to count the occurrences of a subgraph template T in a given network G. The basic problem of computing structural properties such as counting triangles and other subgraphs has found applications in diverse domains.…

In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…

In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…

Learning graph generative models is a challenging task for deep learning and has wide applicability to a range of domains like chemistry, biology and social science. However current deep neural methods suffer from limited scalability: for a…

Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…

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…

In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…

We present a succinct data structure for permutation graphs, and their superclass of circular permutation graphs, i.e., data structures using optimal space up to lower order terms. Unlike concurrent work on circle graphs (Acan et al. 2022),…

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…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…

Gaussian Boson Sampling (GBS) is a quantum computing concept based on drawing samples from a multimode nonclassical Gaussian state using photon-number resolving detectors. It was initially posed as a near-term approach aiming to achieve…

We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…

Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms.…

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…

Motivation: Precision medicine is a major trend in the future of medicine. It aims to provide tailored medical treatment and prevention strategies based on an individual's unique characteristics and needs. Biomarker is the primary source of…

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing…