Results 91 to 100 of about 1,556 (147)

Rapid GPU-Based Pangenome Graph Layout

SC24: International Conference for High Performance Computing, Networking, Storage and Analysis
Accepted and presented on SC 2024: https://dl.acm.org/doi/10.1109/SC41406.2024 ...
Jiajie Li 0008, Jan-Niklas Schmelzle, Yixiao Du, Simon Heumos, Andrea Guarracino, Giulia Guidi, Pjotr Prins, Erik Garrison, Zhiru Zhang   +8 more
openaire   +2 more sources

TIPE: A Bounded and Signature-Aware Framework for Path Construction in Genome Graphs

IEEE Access
Graph-based representations are increasingly used to model genomic variation, enabling richer descriptions than linear reference sequences. However, scalable enumeration and indexing of paths in such graphs remain challenging due to the combinatorial ...
Dimitris Kalatzis
doaj   +1 more source

Pangenome comparison via ED strings

Frontiers in Bioinformatics
IntroductionAn elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings.
Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba   +7 more
doaj   +1 more source

vgteam/sv-genotyping-paper: Code repository for "Genotyping structural variants in pangenome graphs using the vg toolkit" [PDF]

, 2019
<p>This repository contains the commands and scripts used for <a href="https://jmonlong.github.io/manu-vgsv/v/35852320569f679f1ded48e162a4b7f48a9cb158/">Genotyping structural variants in pangenome graphs using the vg toolkit, 2019</a> (&
Jean Monlong, Glenn Hickey, David Heller
core   +1 more source

Privacy-Preserving Pangenome Graphs

Abstract The human pangenome reference, often represented as a graph, promises to capture genetic diversity across populations, but open release of individual haplotypes raises significant privacy concerns, including risks of re-identification and inference of sensitive traits.
Jacob Blindenbach, Shaunak Soni, Gamze Gürsoy   +2 more
openaire   +1 more source

Pangenome graph construction from genome alignments with Minigraph-Cactus [PDF]

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph.
Paten, Benedict
core   +4 more sources

Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes

Genetics Selection Evolution
Background The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic ...
Valentin Sorin, Maulana Mughitz Naji, Clément Birbes, Cécile Grohs, Clémentine Escouflaire, Sébastien Fritz, Camille Eché, Camille Marcuzzo, Amandine Suin, Cécile Donnadieu, Christine Gaspin, Carole Iampietro, Denis Milan, Laurence Drouilhet, Gwenola Tosser-Klopp, Didier Boichard, Christophe Klopp, Marie-Pierre Sanchez, Mekki Boussaha   +18 more
doaj   +1 more source

Approaches to Studying Virus Pangenome Variation Graphs

Genomics, Proteomics & Bioinformatics
Abstract Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here I focus on how PVGs are a powerful tool for studying genetic variation in viruses, offering insights into the complexities of viral quasispecies, mutation rates, and ...
openaire   +3 more sources

Mem-based pangenome indexing for k-mer queries

Algorithms for Molecular Biology
Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations.
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead   +6 more
doaj   +1 more source

Element-based graph pangenome

, 2023
Genomic analyses are based on using a single reference genome that does not represent the whole intraspecies diversity. Instead, a pangenome contains the whole genome content of a species. State-of-art models for pangenome representations are divided into linear and nucleotide-based graph pangenomes. The linear model is composed by the reference genome
openaire   +1 more source