Results 101 to 110 of about 2,351 (162)

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat

Communications Biology
Error self-correction is crucial for analyzing long-read sequencing data, but existing methods often struggle with noisy data or are tailored to technologies like PacBio HiFi.
Yuansheng Liu, Yichen Li, Enlian Chen, Jialu Xu, Wenhai Zhang, Xiangxiang Zeng, Xiao Luo   +6 more
doaj   +1 more source

Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. [PDF]

Bioinformatics, 2021
Khan J, Patro R.
europepmc   +1 more source

A Study of Computational Genome Assembly by Graph Theory

Annals of the West University of Timisoara: Mathematics and Computer Science
The assembly of billions of short sequencing reads into a contiguous genome is a daunting task. The foundation knowledge of current DNA assembly models is concentrated among a select group, where the solution to the genome assembly challenge lies in ...
Sarkar Bijan
doaj   +1 more source

A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification

BioData Mining
Viral species classification is crucial for understanding viral evolution, epidemiology, and developing effective diagnostics and treatments. Traditional methods often rely on sequence similarity, which can be challenging for rapidly evolving viruses ...
Fabio Cumbo, Kabir Dhillon, Jayadev Joshi, Davide Chicco, Sercan Aygun, Daniel Blankenberg   +5 more
doaj   +1 more source

Constrained coding for error mitigation in nanopore-based DNA data storage

Scientific Reports
DNA has been proposed as an alternative to magnetic and solid-state devices for storing digital data. In DNA data storage, writing data is performed through DNA synthesis, and reading is done via sequencing.
Kallie Whritenour, Mete Civelek, Farzad Farnoud   +2 more
doaj   +1 more source

PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs

, 2023
Kuronen J, Horsfield S, Pöntinen AK, Arredondo-Alonso S, Thorpe H, Gladstone R, Willems RJ, Bentley SD, Croucher NJ, Pensar J, Lees JA, Tonkin-Hill G, Corander J.   +12 more
europepmc   +1 more source

Bijections in de Bruijn Graphs

, 2017
A T-net of order $m$ is a graph with $m$ nodes and $2m$ directed edges, where every node has indegree and outdegree equal to $2$. (A well known example of T-nets are de Bruijn graphs.) Given a T-net $N$ of order $m$, there is the so called "doubling" process that creates a T-net $N^*$ from $N$ with $2m$ nodes and $4m$ edges. Let $|X|$ denote the number
openaire   +2 more sources

K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets. [PDF]

Bioinform Adv
Vandamme L, Cazaux B, Limasset A.
europepmc   +1 more source

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs

, 2023
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C.   +5 more
europepmc   +1 more source

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs^. [PDF]

J Comput Biol
Campanelli A, Pibiri GE, Fan J, Patro R.
europepmc   +1 more source