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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
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Вавиловский журнал генетики и селекции, 2021 Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation.
A. Yu. Pronozin +2 more
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The bacterial pangenome as a new tool for analysing pathogenic bacteria
New Microbes and New Infections, 2015 The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and
Didier Raoult +2 more
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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
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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 ...
Zuyu Yang +12 more
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Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference
Life, 2023 A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material.
Paolo Abondio +2 more
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A pangenome analysis pipeline provides insights into functional gene identification in rice
Genome Biology, 2023 Background A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of
Jian Wang +14 more
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A super-pangenome of the North American wild grape species
Genome Biology, 2023 Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic
Noé Cochetel +10 more
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Protocol for post-processing of bacterial pangenome data using Pagoo pipeline
STAR Protocols, 2021 Summary: Multiple downstream analyses are necessary to interpret the output of bacterial pangenome reconstruction software. This requires integrating diverse kinds of genetic and phenotypic data, which to date are left to each user’s criterion.
Ignacio Ferrés, Gregorio Iraola
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Journal of Animal Science and Biotechnology, 2023 As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.
Ying Gong +4 more
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