Genome graphs and the evolution of genome inference [PDF]
Genome Research, 2017 Abstract The human reference genome is part of the foundation of modern human biology, and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics.
Adam M Novak +2 more
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Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis [PDF]
Nature Communications, 2022 Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain ...
H. Serhat Tetikol +11 more
doaj +3 more sources
GenGraph: a python module for the simple generation and manipulation of genome graphs [PDF]
BMC Bioinformatics, 2019 Background As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate ...
Jon Mitchell Ambler +2 more
doaj +5 more sources
BubbleGun: enumerating bubbles and superbubbles in genome graphs [PDF]
Bioinformatics, 2022 Abstract Motivation With the fast development of sequencing technology, accurate de novo genome assembly is now possible even for larger genomes. Graph-based representations of genomes arise both as part of the assembly process, but also in the context of pangenomes representing a population ...
Jana Ebler +2 more
exaly +5 more sources
Gramtools enables multiscale variation analysis with genome graphs [PDF]
Genome Biology, 2021 Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can
Brice Letcher, Martin Hunt, Zamin Iqbal
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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
Accurate sequence variant genotyping in cattle using variation-aware genome graphs [PDF]
Genetics Selection Evolution, 2019 Background Genotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear reference genome. Because a linear reference genome represents only a small fraction of all the DNA sequence variation within a ...
Danang Crysnanto +2 more
doaj +2 more sources
Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [PDF]
Cell Genomics, 2023 Cristian Groza +2 more
exaly +2 more sources
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs [PDF]
Cell, 2020 Franklin Huang, Nicolas Robine
exaly +2 more sources
MGA: a tool for haplotype-mixed assembly of long and accurate reads [PDF]
Genome BiologyRecent large-scale genome sequencing projects have generated near-complete diploid assemblies that reconstruct both haplomes. Producing such assemblies remains formidable, typically requiring large teams, extensive manual curation, and integration of ...
Zhenmiao Zhang +3 more
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