Results 11 to 20 of about 1,556 (147)
Annual Review of Genomics and Human Genetics, 2020 Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes.
Adam M Novak +2 more
exaly +11 more sources
AlfaPang: alignment free algorithm for pangenome graph construction [PDF]
Algorithms for Molecular BiologyThe success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections.
Adam Cicherski +2 more
exaly +10 more sources
GBZ file format for pangenome graphs [PDF]
Bioinformatics, 2022 Abstract Motivation Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space-efficiently.
Jouni Siren +2 more
exaly +12 more sources
Constructing and personalizing population pangenome graphs [PDF]
Nature MethodsPangenome graphs signify a new frontier in genome representation. Recent advances in constructing and personalizing them mark progress in this area.
Yoann Dufresne +2 more
exaly +6 more sources
PangeBlocks: customized construction of pangenome graphs via maximal blocks [PDF]
BMC BioinformaticsBackground The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization ...
Jorge Avila Cartes +4 more
doaj +3 more sources
Maximum-scoring path sets on pangenome graphs of constant treewidth [PDF]
Frontiers in BioinformaticsWe generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139–150), from sequences to graphs.
Broňa Brejová +3 more
doaj +5 more sources
Unbiased pangenome graphs [PDF]
Bioinformatics, 2023 Abstract Motivation Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments.
Andrea Guarracino +2 more
exaly +5 more sources
Building pangenome graphs [PDF]
Nature Methods, 2023 Abstract Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-
Erik Garrison +29 more
core +10 more sources
ODGI: understanding pangenome graphs [PDF]
Bioinformatics, 2022 Abstract Motivation Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions.
Andrea Guarracino +2 more
exaly +5 more sources
Pangenome graphs improve the analysis of structural variants in rare genetic diseases [PDF]
Nature CommunicationsRare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-
Cristian Groza +10 more
doaj +3 more sources