Detecting high-scoring local alignments in pangenome graphs. [PDF]
Bioinformatics, 2021 Abstract Motivation Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence ...
Schulz T +4 more
europepmc +8 more sources
Construction and representation of human pangenome graphs [PDF]
, 2023 Abstract As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses.
Andreace, Francesco +3 more
openaire +2 more sources
Genotyping structural variants in pangenome graphs using the vg toolkit [PDF]
Genome Biology, 2020 Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs ...
Glenn Hickey +9 more
doaj +2 more sources
GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs [PDF]
Nature Communications, 2019 Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be ...
Hannes P. Eggertsson +9 more
doaj +2 more sources
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers [PDF]
BMC BioinformaticsBackground Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes/edges, growth curves ...
Tristan Cumer +3 more
doaj +2 more sources
Differential quantification of alternative splicing events on spliced pangenome graphs. [PDF]
PLoS Computational BiologyPangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of a population, thus reducing the bias introduced by a single reference genome.
Simone Ciccolella +5 more
doaj +2 more sources
Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes [PDF]
Nature CommunicationsPangenome projects have enhanced our understanding of human genomic and genetic diversity, but repetitive regions are still challenging to assemble and yet medically important.
Yoshihiko Suzuki +8 more
doaj +2 more sources
Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia [PDF]
Scientific DataThe selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here
Maxat Kulmanov +13 more
doaj +2 more sources
Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies [PDF]
Journal of Animal Science and BiotechnologyStructural variations (SVs ≥ 50 bp) are a critical but underexplored source of genetic diversity in cattle, shaping traits vital for productivity, adaptability, and health. Advances in long-read sequencing, pangenome graph construction, and near-complete
George E. Liu
doaj +2 more sources
A graph-based approach for the visualisation and analysis of bacterial pangenomes [PDF]
BMC Bioinformatics, 2022 Background The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species.
Joshua D. Harling-Lee +5 more
doaj +3 more sources