Comparing methods for constructing and representing human pangenome graphs [PDF]
Genome Biology, 2023 Background 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.
Francesco Andreace, Chikhi Rayan
exaly +8 more sources
Co-linear chaining on pangenome graphs [PDF]
Algorithms for Molecular Biology, 2023 Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack.
Jyotshna Rajput +2 more
exaly +9 more sources
Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads [PDF]
Frontiers in Genetics, 2023 Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are ...
Andrea Guarracino +2 more
exaly +7 more sources
Complexity welcome: Pangenome graphs for comprehensive population genomics [PDF]
Quantitative Plant BiologyPangenome graphs are revolutionising evolutionary and population genomics by moving beyond linear reference genomes to represent the full spectrum of sequence diversity within and across species.
Zhigui Bao, Detlef Weigel
doaj +5 more sources
The design and construction of reference pangenome graphs with minigraph [PDF]
Genome Biology, 2020 The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists ...
Heng Li, Xiaowen Feng, Chong Chu
doaj +5 more sources
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs. [PDF]
PLoS Computational Biology, 2021 Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS).
Manuel Tognon +4 more
doaj +6 more sources
Beyond single references: pangenome graphs and the future of genomic medicine [PDF]
Frontiers in GeneticsGenomic medicine relies on single reference genomes that miss crucial genetic diversity, creating diagnostic gaps that disproportionately affect underrepresented populations.
Denis M. Nyaga +4 more
doaj +2 more sources
On the optimization of copy number variations representation in pangenome graphs [PDF]
Frontiers in BioinformaticsGraph-based pangenome references often misrepresent Copy Number Variations (CNVs) and Variable Number Tandem Repeats (VNTRs) as alternative acyclic paths, which hinders downstream analyses, degrades alignment behavior, and reduces interpretability in ...
Mirko Coggi +7 more
doaj +2 more sources
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle [PDF]
Nature CommunicationsStructural variants are an underexplored source of genetic diversity. As part of the FarmGTEx Project, here we report a Holstein breed-specific pangenome graph (H20D) using Minigraph-Cactus and 40 phased haploid assemblies from 20 cows.
Liu Yang +14 more
doaj +2 more sources
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs [PDF]
Nature Communications, 2021 Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph.
Tsung-Yu Lu +2 more
doaj +2 more sources