Results 11 to 20 of about 11,936 (226)

Personalized Pangenome References [PDF]

Nature Methods, 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, Eskandar, Parsa, Chang, Xian, Eizenga, Jordan M, Chang, Pi-Chuan, Paten, Benedict, Kolmogorov, Mikhail, Ungaro, Matteo Tommaso, Sirén, Jouni, Monlong, Jean, Hickey, Glenn, Novak, Adam M   +11 more
core   +8 more sources

Building pangenome graphs [PDF]

Nature Methods, 2023
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.
Guarracino, A., Weigel, D. ; https://orcid.org/, Rusholme-Pilcher, R., Nobrega, F., Williams, R., Hagmann, J. ; https://orcid.org/, Golicz, A., Vorbrugg, S. ; https://orcid.org/, Yang, Z., Liti, G., Mwaniki, M., Villani, F., Wu, Y., Heumos, S., Huang, S., Kubica, C. ; https://orcid.org/, Nahnsen, S., Prins, P., Bao, Z. ; https://orcid.org/, Tattini, T., Garrison, E., Marco-Sola, S., Rudbeck, E., Sudmant, P., Chen, H., Soranzo, N., Ashbrook, G., Thorell, K., Colonna, V., de Ligt, J.   +29 more
core   +8 more sources

Bacterial microevolution and the Pangenome [PDF]

, 2020
The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome.
Xavier Didelot, Didelot, Xavier, Florent Lassalle, Lassalle, Florent   +3 more
core   +3 more sources

The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species [PDF]

Genome Biology, 2023
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-
Timothy P. L. Smith, Derek M. Bickhart, Didier Boichard, Amanda J. Chamberlain, Appolinaire Djikeng, Yu Jiang, Wai Y. Low, Hubert Pausch, Sebastian Demyda-Peyrás, James Prendergast, Robert D. Schnabel, Benjamin D. Rosen, Bovine Pangenome Consortium   +12 more
doaj   +5 more sources

Pangenome-aware DeepVariant [PDF]

Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium,
Carroll, Andrew, Paten, Benedict, Asri, Mobin, Brambrink, Lucas, Kolesnikov, Alexey, Sirén, Jouni, Novak, Adam M, Dorfman, Lizzie, Eskandar, Parsa, Webster, Dale R, Shafin, Kishwar, Chang, Pi-Chuan, Mier, Juan Carlos, Cook, Daniel E, Hickey, Glenn   +14 more
core   +4 more sources

PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome [PDF]

BMC Genomics
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated ...
Mingwei Liu, Fan Zhang, Huimin Lu, Hongzhang Xue, Xiaorui Dong, Zhikang Li, Jianlong Xu, Wensheng Wang, Chaochun Wei   +8 more
doaj   +2 more sources

Bacterial Pangenome

Проблемы особо опасных инфекций
This literature review provides an aggregate data on pan-genome studies since the early 2000s. In molecular biology and genetics, pan-genome is the totality of all genetic information on a group of organisms (species or monophyletic group of organisms ...
E. Yu. Agafonova
doaj   +2 more sources

Construction and representation of human pangenome graphs [PDF]

, 2023
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.
Dufresne, Yoann, Chikhi, Rayan, Andreace, Francesco, Lechat, Pierre   +3 more
core   +1 more source

Legume Pangenome: Status and Scope for Crop Improvement [PDF]

, 2022
In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major ...
Mahendar Thudi, Uday Chand Jha, Yogesh Dashrath Naik, Nayyar, Harsh, Siddique, Kadambot H. M., Eric J. B. von Wettberg, Jha, Uday Chand, Thudi, Mahendar, von Wettberg, Eric J. B., Naik, Yogesh Dashrath, Harsh Nayyar, Kadambot H. M. Siddique   +11 more
core   +1 more source

Unbiased pangenome graphs [PDF]

Bioinformatics, 2022
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.
Erik Garrison, Andrea Guarracino
openaire   +2 more sources