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Computational graph pangenomics: a tutorial on data structures and their applications [PDF]
Natural Computing, 2022 AbstractComputational pangenomics is an emerging research field that is changing the way computer scientists are facing challenges in biological sequence analysis. In past decades, contributions from combinatorics, stringology, graph theory and data structures were essential in the development of a plethora of software tools for the analysis of the ...
Jasmijn A. Baaijens +6 more
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, 2023 The two GIFs show a snapshot after each epoch of the Path-Guided Stochastic Gradient Descent (PG-SGD) algorithm which is described in https://github.com/pangenome/sorting-paper.
Simon Heumos +2 more
core +1 more source
Nature Communications, 2022 The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low ...
Justin N. Vaughn +6 more
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Panakeia - a universal tool for bacterial pangenome analysis
BMC Genomics, 2022 Background Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years.
Sina Beier, Nicholas R Thomson
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Towards an edit distance between pangenome graphs [PDF]
, 2023 National audienceA variation graph is a data structure that aims to represent variations among a collection of genomes. It is a sequence graph where each genome is embedded as a path in the graph with the successive nodes, along the path, corresponding ...
Faraut, Thomas +4 more
core +8 more sources
Semantic Variation Graphs: Ontologies for Pangenome Graphs [PDF]
, 2020 Background: Variation graphs are a novel way to describe genomic variation across a population. Variation graph tools present a significant improvement in mitigating reference bias compared to the linear reference ecosystem.
Trybushnyi, Dmytro +7 more
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Towards an edit distance between pangenome graphs [PDF]
International audienceA pangenome graph is a sequence graph that aims to represent variations among a collection of genomes in a single data structure. Each genome is segmented and embedded as a path in the graph with its successive nodes corresponding ...
Thomas, Faraut +3 more
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GraphAligner: rapid and versatile sequence-to-graph alignment
Genome Biology, 2020 Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph.
Mikko Rautiainen, Tobias Marschall
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Establishing Bovine Pangenome Graphs
, 2021 The assembly of the draft Bos taurus reference genome was a milestone for genetics- and genomics-oriented research in cattle. The reference genome of domestic cattle was built from a single animal from the Hereford breed. However, the linear reference sequence does not represent the genetic diversity of global cattle breeds.
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Personalized Pangenome References [PDF]
, 2023 Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for
Carroll, Andrew +11 more
core +1 more source